Locus 1376

Sequence ID 3R_DroMel_CAF1
Location 4,011,481 – 4,011,669
Length 188
Max. P 0.941805
window2266 window2267 window2268 window2269

overview

Window 6

Location 4,011,481 – 4,011,589
Length 108
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 86.22
Mean single sequence MFE -27.66
Consensus MFE -19.25
Energy contribution -20.75
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.70
SVM decision value 0.21
SVM RNA-class probability 0.635950
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4011481 108 + 27905053
CCCCUUCGGUUACUCCGCCCCUGGAUCAGCCAAUC----CCCC-----CUAGCCCCCUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCA
.......((((..((((....))))..))))....----....-----...(((....(((((.....(((((........))))).......))))).))).((((.....)))). ( -27.90)
>DroSec_CAF1 17158 108 + 1
CCCCUUGGGUUACUCCGCCCCUGGAUCUGCCAACC----CCCC-----CUAGCCCCCUUCGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCA
..((..((((......))))..))...(((((...----....-----...(((......))).....(((((........)))))............)))))((((.....)))). ( -28.00)
>DroSim_CAF1 17734 103 + 1
C-CCUUGGGUUACUCC--CCCUGGAUCUGCCAACC----C-CC-----CUAGCCC-CUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCA
.-((..(((......)--))..))...........----.-..-----...(((.-..(((((.....(((((........))))).......))))).))).((((.....)))). ( -27.30)
>DroYak_CAF1 17393 116 + 1
CCCCCUGGGUUACUCCGCCCCUGGAUUUGACCCCCGUGCCCCGCUCUUCGAA-CCCCUUUAGCCACCAACUGUUAGCGACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCA
......((((((.((((....))))..))))))..(((....(((.......-.......))).....(((((........))))).)))..((((...))))((((.....)))). ( -27.44)
>consensus
CCCCUUGGGUUACUCCGCCCCUGGAUCUGCCAACC____CCCC_____CUAGCCCCCUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCA
..((..((((......))))..))...........................(((......))).....(((((........)))))......((((...))))((((.....)))). (-19.25 = -20.75 +   1.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,011,517 – 4,011,629
Length 112
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 92.58
Mean single sequence MFE -29.73
Consensus MFE -25.94
Energy contribution -26.25
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.87
SVM decision value 1.32
SVM RNA-class probability 0.941805
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4011517 112 + 27905053
CCC-----CUAGCCCCCUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUU
...-----.(((((....(((((.....(((((........))))).......)))))(((((((((.....)))).(((....)))........))))))))))............ ( -32.70)
>DroSec_CAF1 17194 112 + 1
CCC-----CUAGCCCCCUUCGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGACUAUAAAUGUAAAUU
...-----...(((......)))..((((((((........)))))............(((((((((.....)))).(((....)))........))))).........)))..... ( -24.90)
>DroSim_CAF1 17767 110 + 1
-CC-----CUAGCCC-CUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUU
-..-----.(((((.-..(((((.....(((((........))))).......)))))(((((((((.....)))).(((....)))........))))))))))............ ( -32.70)
>DroYak_CAF1 17433 116 + 1
CCGCUCUUCGAA-CCCCUUUAGCCACCAACUGUUAGCGACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUU
............-......(((((....(((((........)))))............(((((((((.....)))).(((....)))........))))))))))............ ( -28.60)
>consensus
CCC_____CUAGCCCCCUUUGGCCAACAACUGUUACCAACUGCAGUACACACCGCCAAUGGCGGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUU
...................(((((....(((((........)))))............(((((((((.....)))).(((....)))........))))))))))............ (-25.94 = -26.25 +   0.31)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,011,517 – 4,011,629
Length 112
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 92.58
Mean single sequence MFE -41.65
Consensus MFE -37.00
Energy contribution -37.50
Covariance contribution 0.50
Combinations/Pair 1.09
Mean z-score -2.01
Structure conservation index 0.89
SVM decision value 1.22
SVM RNA-class probability 0.932420
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4011517 112 - 27905053
AAUUUACAUUUAUAGCCUGGCGCAUGAGGUGCUUACGAGCUGCACAGGAUGUGCCGCCAUUGGCGGUGUGUACUGCAGUUGGUAACAGUUGUUGGCCAAAGGGGGCUAG-----GGG
............(((((((((.((..((.((.((((.(((((((....(((..(((((...)))))..)))..))))))).)))))).))..))))).....)))))).-----... ( -42.30)
>DroSec_CAF1 17194 112 - 1
AAUUUACAUUUAUAGUCUGGCGCAUGAGGUGCUUACGAGCUGCACAGGAUGUGCCGCCAUUGGCGGUGUGUACUGCAGUUGGUAACAGUUGUUGGCCGAAGGGGGCUAG-----GGG
...............((((((.((..((.((.((((.(((((((....(((..(((((...)))))..)))..))))))).)))))).))..)).((....)).)))))-----).. ( -40.30)
>DroSim_CAF1 17767 110 - 1
AAUUUACAUUUAUAGCCUGGCGCAUGAGGUGCUUACGAGCUGCACAGGAUGUGCCGCCAUUGGCGGUGUGUACUGCAGUUGGUAACAGUUGUUGGCCAAAG-GGGCUAG-----GG-
............(((((((((.((..((.((.((((.(((((((....(((..(((((...)))))..)))..))))))).)))))).))..)))))....-)))))).-----..- ( -42.70)
>DroYak_CAF1 17433 116 - 1
AAUUUACAUUUAUAGCCUGGCGCAUGAGGUGCUUACGAGCUGCACAGGAUGUGCCGCCAUUGGCGGUGUGUACUGCAGUCGCUAACAGUUGGUGGCUAAAGGGG-UUCGAAGAGCGG
..............(((((((((.....)))))..((((((.(.(((.(((..(((((...)))))..))).))).((((((((.....))))))))...).))-)))).)).)).. ( -41.30)
>consensus
AAUUUACAUUUAUAGCCUGGCGCAUGAGGUGCUUACGAGCUGCACAGGAUGUGCCGCCAUUGGCGGUGUGUACUGCAGUUGGUAACAGUUGUUGGCCAAAGGGGGCUAG_____GGG
............(((((((((.((..((.((.((((.(((((((....(((..(((((...)))))..)))..))))))).)))))).))..))))).....))))))......... (-37.00 = -37.50 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,011,552 – 4,011,669
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.22
Mean single sequence MFE -34.92
Consensus MFE -33.12
Energy contribution -33.04
Covariance contribution -0.08
Combinations/Pair 1.11
Mean z-score -1.17
Structure conservation index 0.95
SVM decision value 0.40
SVM RNA-class probability 0.720772
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4011552 117 + 27905053
UGCAGUACACACCGCCAAUGGC---GGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUUGCCUAAAUGGGCAAAAGCUCGAGCAUACGUUGGCCAGGAC
...........(((((((((..---.((((.....)))).(((((..(((.(((........))).............((((((....))))))..))))))))...)))))))..)).. ( -37.20)
>DroSec_CAF1 17229 117 + 1
UGCAGUACACACCGCCAAUGGC---GGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGACUAUAAAUGUAAAUUGCCUAAAUGGGCAAAAGCUCGAGCAUACGUUGGCCAGGAC
...........(((((((((..---.((((.....)))).(((((..(((..............((.......))...((((((....))))))..))))))))...)))))))..)).. ( -35.30)
>DroSim_CAF1 17800 117 + 1
UGCAGUACACACCGCCAAUGGC---GGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUUGCCUAAAUGGGCAAAAGCUCGAGCAUACGUUGGCCAGGAC
...........(((((((((..---.((((.....)))).(((((..(((.(((........))).............((((((....))))))..))))))))...)))))))..)).. ( -37.20)
>DroWil_CAF1 10824 109 + 1
-----------UCGCCAAUGGCUGUGGCAUAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUUGCCUAAAUGGGUAGAAGCUCGAGCAUACGUUGCCCUCUAC
-----------..((..((((((.((((.(((...((((.........))))...))).)))))))))).((((((..((((((....))))))..((....)).))))))))....... ( -27.70)
>DroYak_CAF1 17472 117 + 1
UGCAGUACACACCGCCAAUGGC---GGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUUGCCUAAAUGGGCAAAAGCUCGAGCAUACGUUGGCCAGGAC
...........(((((((((..---.((((.....)))).(((((..(((.(((........))).............((((((....))))))..))))))))...)))))))..)).. ( -37.20)
>consensus
UGCAGUACACACCGCCAAUGGC___GGCACAUCCUGUGCAGCUCGUAAGCACCUCAUGCGCCAGGCUAUAAAUGUAAAUUGCCUAAAUGGGCAAAAGCUCGAGCAUACGUUGGCCAGGAC
.............(((((((......((((.....)))).(((((..(((.(((........))).............((((((....))))))..))))))))...)))))))...... (-33.12 = -33.04 +  -0.08)

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 10:08:31 2006