Locus 1277

Sequence ID 3R_DroMel_CAF1
Location 3,790,840 – 3,791,000
Length 160
Max. P 0.995978
window2087 window2088 window2089 window2090

overview

Window 7

Location 3,790,840 – 3,790,960
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.42
Mean single sequence MFE -32.88
Consensus MFE -26.65
Energy contribution -26.29
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -2.82
Structure conservation index 0.81
SVM decision value 2.64
SVM RNA-class probability 0.995978
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790840 120 + 27905053
UAAUGACAAAUAUAAGCAGGGAAACAGUGGUCAAAGUUGCCAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUC
....(((((((....((..(....).((((((((..(..((...........))...)..))))))))..))(((((((....((((((.....)))))).))))))).....))))))) ( -35.90)
>DroSec_CAF1 20256 118 + 1
UGAUGACAAAUAUCA--AGGGAAACAGUUGUCAAAGUUGCCAGAGGAAAAGCGGAUUAAAUUGAUUACGGGUGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUC
....(((((((((((--(.(....)....(((...(((.((...))...))).)))....)))))......((((((((....((((((.....)))))).))))))))....))))))) ( -31.10)
>DroSim_CAF1 24746 118 + 1
UGAUGACAAAUAUCA--AGGGAAACAGUUGUCAAAGUUGCCAGAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUU
....(((((((((((--(.(....)....(((...(((.((...))...))).)))....))))).......(((((((....((((((.....)))))).))))))).....))))))) ( -29.10)
>DroEre_CAF1 10868 117 + 1
UAAUGACAAGUAUCU--AGGGAAACAGCU-CCGCAGUUGCCAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUC
....(((((((....--..(....).(((-((((..((.(....).))..)))((((.....))))..))))(((((((....((((((.....)))))).))))))).....))))))) ( -33.70)
>DroYak_CAF1 22377 117 + 1
UUAUGACAAGAAUCA--AGGGUAACAGCU-CCGCAGUUGCCAAAGGAGAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUC
....(((((((((((--(...(((....(-((((..((.(....).))..))))))))..))))))......(((((((....((((((.....)))))).)))))))......)))))) ( -34.60)
>consensus
UAAUGACAAAUAUCA__AGGGAAACAGUUGUCAAAGUUGCCAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUC
....(((((((........(....).............(((...(......................).)))(((((((....((((((.....)))))).))))))).....))))))) (-26.65 = -26.29 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,790,840 – 3,790,960
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.42
Mean single sequence MFE -24.68
Consensus MFE -19.54
Energy contribution -19.58
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.79
SVM decision value 1.05
SVM RNA-class probability 0.906063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790840 120 - 27905053
GACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUGGCAACUUUGACCACUGUUUCCCUGCUUAUAUUUGUCAUUA
(((((((....(((((((((..((....)).(((.(.....).)))......))).............(((........)))....................)))))).))))))).... ( -22.40)
>DroSec_CAF1 20256 118 - 1
GACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCACCCGUAAUCAAUUUAAUCCGCUUUUCCUCUGGCAACUUUGACAACUGUUUCCCU--UGAUAUUUGUCAUCA
(((((((....((((((((.(((.((.....)).)))....))))))))......(((((........(((........)))......(((....)))....)--))))))))))).... ( -24.50)
>DroSim_CAF1 24746 118 - 1
AACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUCUGGCAACUUUGACAACUGUUUCCCU--UGAUAUUUGUCAUCA
............(((((((.(((.((.....)).)))....)))))))....................(((........))).....((((((.((((.....--.)))).))))))... ( -22.70)
>DroEre_CAF1 10868 117 - 1
GACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUGGCAACUGCGG-AGCUGUUUCCCU--AGAUACUUGUCAUUA
(((((.......(((((((.(((.((.....)).)))....)))))))....(((..........(((((..((((...)).))..))))-).(((......)--)).)))))))).... ( -26.30)
>DroYak_CAF1 22377 117 - 1
GACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUCUCCUUUGGCAACUGCGG-AGCUGUUACCCU--UGAUUCUUGUCAUAA
(((((.......(((((((.(((.((.....)).)))....)))))))....(.((((((........((..((((...(....)...))-))..)).....)--))))))))))).... ( -27.52)
>consensus
GACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUGGCAACUUUGACAACUGUUUCCCU__UGAUAUUUGUCAUCA
(((((......((((((((.(((.((.....)).)))....))))))))...................(((........))).............................))))).... (-19.54 = -19.58 +   0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,790,880 – 3,791,000
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.17
Mean single sequence MFE -30.10
Consensus MFE -26.84
Energy contribution -26.72
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.83
Structure conservation index 0.89
SVM decision value 1.70
SVM RNA-class probability 0.973091
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790880 120 + 27905053
CAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUCUAAAGCGGAAGAGAUCACGAUAAGAACCCACUUCAGGUUA
....................((((....(((.(((((((....((((((.....)))))).)))))))......((((((.....(....).......))))))..)))...)))).... ( -28.40)
>DroSec_CAF1 20294 120 + 1
CAGAGGAAAAGCGGAUUAAAUUGAUUACGGGUGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUCUAAAGCGGAAGAGAUCACGAUAAGAACCCACUUCAGGUUA
..((((.......((((.....))))..(((((((((((....((((((.....)))))).)))))))......((((((.....(....).......)))))).)))).))))...... ( -32.10)
>DroSim_CAF1 24784 120 + 1
CAGAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUUUAAAGCGGAAGAGAUCACGAUAAGAACCCACUUCAGGUUA
..((((..(((((((((((.(((....)))..(((((((....((((((.....)))))).)))))))..)))))))))))....(....)...................))))...... ( -29.40)
>DroEre_CAF1 10905 120 + 1
CAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUCUAAAGCGGAAGAGAUCAUGAUAAGAACCCACUUCAGGUUA
....................((((....(((.(((((((....((((((.....)))))).)))))))......((((((.....(....).......))))))..)))...)))).... ( -29.10)
>DroYak_CAF1 22414 120 + 1
CAAAGGAGAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUCUCAAGCGGAAGAGAUCACGAUAAGAAUGCACUUCAGGUUA
.......((((.(.(((..((((.........(((((((....((((((.....)))))).))))))).........(((((........)))))..))))...))).).))))...... ( -31.50)
>consensus
CAAAGGAAAAGCGGAUUAAAUUGAUUACGGGCGAGCAUAAAAAAUGUGCAGCUUGCGCAUGUAUGCUCAAUUAAUUUGUCUAAAGCGGAAGAGAUCACGAUAAGAACCCACUUCAGGUUA
....................((((....(((.(((((((....((((((.....)))))).)))))))......((((((.....(....).......))))))..)))...)))).... (-26.84 = -26.72 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,790,880 – 3,791,000
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -24.64
Consensus MFE -22.90
Energy contribution -22.82
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -1.40
Structure conservation index 0.93
SVM decision value 0.88
SVM RNA-class probability 0.872552
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790880 120 - 27905053
UAACCUGAAGUGGGUUCUUAUCGUGAUCUCUUCCGCUUUAGACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUG
....((((((((((.((.......)).....))))))))))...........(((((((.(((.((.....)).)))....)))))))((...(((.....)))....)).......... ( -24.90)
>DroSec_CAF1 20294 120 - 1
UAACCUGAAGUGGGUUCUUAUCGUGAUCUCUUCCGCUUUAGACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCACCCGUAAUCAAUUUAAUCCGCUUUUCCUCUG
....((((((((((.((.......)).....))))))))))..........((((((((.(((.((.....)).)))....))))))))............................... ( -25.20)
>DroSim_CAF1 24784 120 - 1
UAACCUGAAGUGGGUUCUUAUCGUGAUCUCUUCCGCUUUAAACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUCUG
......((((((((((.(((..(((........)))..)))...........(((((((.(((.((.....)).)))....)))))))...............))))))))))....... ( -24.30)
>DroEre_CAF1 10905 120 - 1
UAACCUGAAGUGGGUUCUUAUCAUGAUCUCUUCCGCUUUAGACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUG
....((((((((((.((.......)).....))))))))))...........(((((((.(((.((.....)).)))....)))))))((...(((.....)))....)).......... ( -24.90)
>DroYak_CAF1 22414 120 - 1
UAACCUGAAGUGCAUUCUUAUCGUGAUCUCUUCCGCUUGAGACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUCUCCUUUG
......((((((...(((((.((.((.....))))..)))))..........(((((((.(((.((.....)).)))....)))))))...................))))))....... ( -23.90)
>consensus
UAACCUGAAGUGGGUUCUUAUCGUGAUCUCUUCCGCUUUAGACAAAUUAAUUGAGCAUACAUGCGCAAGCUGCACAUUUUUUAUGCUCGCCCGUAAUCAAUUUAAUCCGCUUUUCCUUUG
......((((((((((......(((........)))...............((((((((.(((.((.....)).)))....))))))))..............))))))))))....... (-22.90 = -22.82 +  -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 10:05:31 2006