Locus 2093

Sequence ID 3R_DroMel_CAF1
Location 5,970,605 – 5,970,794
Length 189
Max. P 0.946568
window3423 window3424 window3425

overview

Window 3

Location 5,970,605 – 5,970,725
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.91
Mean single sequence MFE -37.70
Consensus MFE -33.10
Energy contribution -34.14
Covariance contribution 1.04
Combinations/Pair 1.02
Mean z-score -1.34
Structure conservation index 0.88
SVM decision value 0.38
SVM RNA-class probability 0.711316
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5970605 120 + 27905053
UCGGGUAUGGCAGUGAGUCCUACAGAAUGCUCUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUCCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCUGU
..(((....((((((((..(........)..))))))))..(((((.....)).(((((((.(((....))))))))))..))))))....(((((.((((((.....)))))).))))) ( -36.20)
>DroSec_CAF1 21877 119 + 1
UCGGGAAUGGCAGUGAGUCCUACAGAAUGCUCUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGU
.(((((((.((((((((..(........)..))))))))...............(((((((.(((....)))))))))))))))))..-..(((((.((((((.....)))))).))))) ( -40.10)
>DroSim_CAF1 23561 119 + 1
UCGGGAAUGGCAGUGAGUCCUACAGAAUGCUCUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGU
.(((((((.((((((((..(........)..))))))))...............(((((((.(((....)))))))))))))))))..-..(((((.((((((.....)))))).))))) ( -40.10)
>DroEre_CAF1 23337 120 + 1
UCGGGACUGGCAGUGAGUCCUACAGAAUGCUCUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCUAGUGUGUUCCUGCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCCUU
..(((((((((((((((..(........)..)))))))).)))..(((((....)))))..(((((........)))))..))))((....))(((.((((((.....)))))).))).. ( -37.00)
>DroYak_CAF1 22549 120 + 1
UCGGGACUGGCAGUGAGUCCUACAGAAUGCACUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCCAGUGUGUUCCUGCUCUUGCGGCUAACUGCAGUUUGUAGUUUGCUUU
..((((((((((((((((.(........).))))))))).)))(((((((....))))(((.(((....))).))))))..))))((....))(((.((((((.....)))))).))).. ( -35.10)
>consensus
UCGGGAAUGGCAGUGAGUCCUACAGAAUGCUCUCGCUGCACGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU_UUGCGGCUAACUGCAGUUUGUAGUUUGCUGU
.(((((...((((((((..(........)..))))))))(((((((((((....))))).(.(((....))))..))))))))))).....(((((.((((((.....)))))).))))) (-33.10 = -34.14 +   1.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,970,645 – 5,970,762
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.13
Mean single sequence MFE -32.80
Consensus MFE -26.86
Energy contribution -28.90
Covariance contribution 2.04
Combinations/Pair 1.03
Mean z-score -1.95
Structure conservation index 0.82
SVM decision value 1.36
SVM RNA-class probability 0.946568
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5970645 117 + 27905053
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUCCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUAUGCACA-UUU--UUUUGGCGUGGGCUGAGAUUG
....(((((((((.((((.....))))..(((((((.......)))...(((((((.((((((.....)))))).)))))))......)))).-...--......)))))))))...... ( -32.70)
>DroSec_CAF1 21917 116 + 1
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUGUGCAUU-UUU--UUUUGGCGUGGGCUGAGAUUG
....(((((((((.(((((((.(((....)))))))))).....(((.-(((((((.((((((.....)))))).)))))))......)))..-...--......)))))))))...... ( -33.90)
>DroSim_CAF1 23601 117 + 1
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUGUGCAUU-UUU-UUUUUGGCGUGGGCUGAGAUUG
....(((((((((.(((((((.(((....)))))))))).....(((.-(((((((.((((((.....)))))).)))))))......)))..-...-.......)))))))))...... ( -33.90)
>DroEre_CAF1 23377 115 + 1
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCUAGUGUGUUCCUGCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCCUU----UCAUGCAUU-UUUUUGUUUGGCGUGGGCUGAGAUUA
....(((((((((.......((((...((((((............((....))(((.((((((.....)))))).)))..----....)))))-)...))))...)))))))))...... ( -33.90)
>DroYak_CAF1 22589 116 + 1
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCCAGUGUGUUCCUGCUCUUGCGGCUAACUGCAGUUUGUAGUUUGCUUU----ACUUGCAUACUUUUUUUUUGGCGUGGGCUGAUAUUA
....((((((((....((((((...))))))((((((((((....((....))(((.((((((.....)))))).)))..----....))))))........))))))))))))...... ( -29.60)
>consensus
CGGACAGUUCAUGAGAAUUUGACAUUUAAGUGCGAGUUUGUUCCUGCU_UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUAUGCAUU_UUU_UUUUUGGCGUGGGCUGAGAUUG
....(((((((((.(((((((.(((....)))))))))).....(((..(((((((.((((((.....)))))).)))))))......)))..............)))))))))...... (-26.86 = -28.90 +   2.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,970,685 – 5,970,794
Length 109
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.32
Mean single sequence MFE -32.00
Consensus MFE -24.83
Energy contribution -26.67
Covariance contribution 1.84
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.78
SVM decision value 0.39
SVM RNA-class probability 0.715157
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5970685 109 + 27905053
UUCCUCCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUAUGCACA-UUU--UUUUGGCGUGGGCUGAGAUUGG--------GACACACCCACCCGAAAACAAAAACAAAAAG
......((((((((...(((((((((.........)))))))))...)))...-..(--((((((.(((((.((.(.....--------..).))))))))))))))........))))) ( -30.30)
>DroSec_CAF1 21957 116 + 1
UUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUGUGCAUU-UUU--UUUUGGCGUGGGCUGAGAUUGGCGAACACGGACACACCCACCCGAAAACAAAAACAAAAAG
........-(((((((.((((((.....)))))).)))))))((((((...((-(.(--((((((.(((((.((.(.(((.......))).).)))))))))))))).))).)))))).. ( -36.20)
>DroSim_CAF1 23641 117 + 1
UUCCUGCU-UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUGUGCAUU-UUU-UUUUUGGCGUGGGCUGAGAUUGGCGAACACGGACACACCCACCCGAAAACAAAAACAAAAAG
........-(((((((.((((((.....)))))).)))))))((((((...((-((.-(((((((.(((((.((.(.(((.......))).).)))))))))))))).)))))))))).. ( -35.90)
>DroEre_CAF1 23417 109 + 1
UUCCUGCUUUUGCGGCUAACUGCAGUUUGUAGUUUGCCUU----UCAUGCAUU-UUUUUGUUUGGCGUGGGCUGAGAUUAGC------GGACACACCCACCCGAAAACAAAAACAAAAAG
....(((......(((.((((((.....)))))).)))..----....)))..-(((((((((((.((((((((....))))------(....)..))))))))..)))))))....... ( -30.30)
>DroYak_CAF1 22629 110 + 1
UUCCUGCUCUUGCGGCUAACUGCAGUUUGUAGUUUGCUUU----ACUUGCAUACUUUUUUUUUGGCGUGGGCUGAUAUUAGC------GGACACACCCACCCGAAAACAAAAACAAAAAG
....(((...((.(((.((((((.....)))))).))).)----)...)))...(((.(((((((.((((((((....))))------(....)..))))))))))).)))......... ( -27.30)
>consensus
UUCCUGCU_UUGCGGCUAACUGCAGUUUGUAGUUUGCUGUAGUUUUAUGCAUU_UUU_UUUUUGGCGUGGGCUGAGAUUGGC______GGACACACCCACCCGAAAACAAAAACAAAAAG
....(((..(((((((.((((((.....)))))).)))))))......)))...(((.(((((((.(((((.((...................)))))))))))))).)))......... (-24.83 = -26.67 +   1.84)

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 10:27:16 2006