Locus 8639

Sequence ID 3R_DroMel_CAF1
Location 23,106,104 – 23,106,289
Length 185
Max. P 0.999227
window13873 window13874 window13875

overview

Window 3

Location 23,106,104 – 23,106,217
Length 113
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 89.80
Mean single sequence MFE -30.68
Consensus MFE -27.52
Energy contribution -27.36
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -2.47
Structure conservation index 0.90
SVM decision value 3.45
SVM RNA-class probability 0.999227
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23106104 113 - 27905053
UUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUUUUUUUUAAACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAGUA----UACAUAUCAAACGG
(((((...((((((((((....)))))))))).((((((.....))))))..-...............((((((.(.((......)).).))))))....----......)))))... ( -31.20)
>DroSec_CAF1 9115 111 - 1
UUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUUUUU--UUAACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAGUA----UACAUAUCAAACGG
(((((...((((((((((....)))))))))).((((((.....))))))..-......--.......((((((.(.((......)).).))))))....----......)))))... ( -31.20)
>DroSim_CAF1 10932 110 - 1
UUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUU-UU--UUAACCAUCUGCCAAGUGAACUUCCAGUGGGCAGAAGUA----UACAUAUCAAACGG
(((((...((((((((((....)))))))))).((((((.....))))))..-...-..--.......((((((.(.((......)).).))))))....----......)))))... ( -31.20)
>DroEre_CAF1 9391 113 - 1
UUUGACACAAAAAGUCCA-AACUGGAUUUUUUCGCUGGCAGAUAGCCAGCAU-UUU-UU--UUAACCAUCUGCCAAGUGAAUUUCGGGUGGGUUGGAGUAUAUGUACAUAUCAAACGG
((..((..(((((((((.-....))))))))).((((((.....))))))..-...-..--....(((((((............)))))))))..))(((....)))........... ( -30.80)
>DroYak_CAF1 9385 115 - 1
UUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCACAUAGCCAGCAUAUUU-UU--UUAACCAUCUGCCAACUGAAUUUCGGGUGGGUUGAAGUUUCUGUACAUAUCGAACGG
((..((..((((((((((....)))))))))).((((((.....))))))......-..--....(((((((............)))))))))..))....((((.(.....).)))) ( -29.00)
>consensus
UUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU_UUU_UU__UUAACCAUCUGCCAAGUGAAUUUCCAGUGGGCAGAAGUA____UACAUAUCAAACGG
(((((...((((((((((....)))))))))).((((((.....))))))..................((((((.(.((......)).).))))))..............)))))... (-27.52 = -27.36 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 23,106,140 – 23,106,252
Length 112
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 88.81
Mean single sequence MFE -22.62
Consensus MFE -19.30
Energy contribution -19.14
Covariance contribution -0.16
Combinations/Pair 1.05
Mean z-score -1.76
Structure conservation index 0.85
SVM decision value 1.15
SVM RNA-class probability 0.922250
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23106140 112 - 27905053
-----AACCGAAACCUAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUUUUUUUUAAACCAUCUGCCAAGU
-----...................................((((.((.((((((((((....)))))))))).((((((.....))))))..-.................)).)))). ( -19.30)
>DroSec_CAF1 9151 110 - 1
-----AACCGAAACCCAACCGAAUCCAAGUCUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUUUUU--UUAACCAUCUGCCAAGU
-----....((((.......(((((((.((.......((((((......)))))).....)))))))))))))((((((.....))))))..-......--................. ( -20.11)
>DroSim_CAF1 10968 109 - 1
-----AACCGAAACCCAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU-UUU-UU--UUAACCAUCUGCCAAGU
-----...................................((((.((.((((((((((....)))))))))).((((((.....))))))..-...-..--.........)).)))). ( -19.30)
>DroEre_CAF1 9431 113 - 1
CCGAAAACCGAAAGAUAACCGAAUCCACGACUGCUUGACUUUUGACACAAAAAGUCCA-AACUGGAUUUUUUCGCUGGCAGAUAGCCAGCAU-UUU-UU--UUAACCAUCUGCCAAGU
..((((..(....)......(((((((.(..((...(((((((......)))))))))-..))))))))))))((((((.....))))))..-...-..--................. ( -26.90)
>DroYak_CAF1 9425 115 - 1
CCGAAAACCGAAAGAUAACCGAAUCCACGAUUGUCUGUCUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCACAUAGCCAGCAUAUUU-UU--UUAACCAUCUGCCAACU
........(((((((((..(((........)))..)))))))))....((((((((((....)))))))))).((((((.....))))))......-..--................. ( -27.50)
>consensus
_____AACCGAAACCUAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGGCUCGUAGCCAGCAU_UUU_UU__UUAACCAUCUGCCAAGU
.........................................(((.((.((((((((((....)))))))))).((((((.....))))))....................)).))).. (-19.30 = -19.14 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 23,106,179 – 23,106,289
Length 110
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 91.38
Mean single sequence MFE -28.15
Consensus MFE -21.82
Energy contribution -21.90
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.78
SVM decision value -0.02
SVM RNA-class probability 0.521430
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23106179 110 - 27905053
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAA-------AACCGAAACCUAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGG
...........((..(((.((((((((..........-------...............)))))))).)))..)).....(..((..((((((((((....)))))))))).))..) ( -26.01)
>DroSec_CAF1 9188 110 - 1
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAA-------AACCGAAACCCAACCGAAUCCAAGUCUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGG
..........(((((((..((((((((..........-------...............)))))))...)..)).)))))(..((..((((((((((....)))))))))).))..) ( -24.91)
>DroSim_CAF1 11004 110 - 1
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAA-------AACCGAAACCCAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGG
...........((..(((.((((((((..........-------...............)))))))).)))..)).....(..((..((((((((((....)))))))))).))..) ( -26.01)
>DroEre_CAF1 9467 116 - 1
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAAAGCCGAAAACCGAAAGAUAACCGAAUCCACGACUGCUUGACUUUUGACACAAAAAGUCCA-AACUGGAUUUUUUCGCUGG
..((((..((((((.(((.((((((((....(.(....).)......(....)......)))))))).)))))))))..)))).((((((((((((.-....))))))))).).)). ( -34.30)
>DroYak_CAF1 9462 117 - 1
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAAUGCCGAAAACCGAAAGAUAACCGAAUCCACGAUUGUCUGUCUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGG
......((((...(((((..(((((((.......)))).)))...)))))..)))).......((((((.((((........))))..(((((((((....)))))))))))).))) ( -29.50)
>consensus
AGUAAAUAUCGAGUUGGUGGUGGAUUCUGAAGACGAA_______AACCGAAACCUAACCGAAUCCACGACUGCCUAACUUUUGACACAAAAAGUCCAAAACUGGAUUUUUUCGUUGG
.((........((..(((.((((((((................................)))))))).)))..))........))..((((((((((....))))))))))...... (-21.82 = -21.90 +   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 13:16:02 2006