Locus 1664

Sequence ID X_DroMel_CAF1
Location 4,685,115 – 4,685,263
Length 148
Max. P 0.860761
window2736 window2737 window2738 window2739

overview

Window 6

Location 4,685,115 – 4,685,223
Length 108
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -34.58
Consensus MFE -29.78
Energy contribution -29.72
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -1.80
Structure conservation index 0.86
SVM decision value 0.83
SVM RNA-class probability 0.860761
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4685115 108 + 22224390
CUGCGAA--AUGUCGCUCACAUGCAAUUAAAUUCGCUCAGCUCAGUAAUUUGGAGCUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUA
..(((((--..((.((......)).))....)))))...((((.....(((((.((((((((((.---------...)))))))))))))))..))))..-(((((......)))))... ( -35.10)
>DroSec_CAF1 38739 108 + 1
CUGCGAA--AUGUUGCUCACAUCCAAUUAAAUUCGCUCAGCUCCGUAAUUUGGAGCUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUA
..(((((--..((((........))))....)))))...(((((....(((((.((((((((((.---------...))))))))))))))).)))))..-(((((......)))))... ( -36.90)
>DroEre_CAF1 39135 108 + 1
--ACGAACGAUGUCGCUCACAUGCAAUUAAAUUUGCUCAGCUCAGUAAUUUGGCGUUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUA
--..((.((....)).))....((((......))))...((((.....(((((.((((((((((.---------...)))))))))))))))..))))..-(((((......)))))... ( -31.30)
>DroYak_CAF1 35946 118 + 1
CUGCGAA--AUGUCGCUCACAUGCAAUUAAAUUCGCUCAGCUCAGUAAUUUGGAGCUGUGAAGUUGCCAAAGUUGCCAUUUCGCAGGCCGGAGGGAGCCAAACUCAUGUAAUUGAGUGUA
(((((((--(((..((......(((((....(((((..(((((.........))))))))))))))).......))))))))))))...((......))..(((((......)))))... ( -35.02)
>consensus
CUGCGAA__AUGUCGCUCACAUGCAAUUAAAUUCGCUCAGCUCAGUAAUUUGGAGCUGUGAAGUU_________UCCAUUUCGCAGCCCGGGGGGAGCCA_ACUCAUGUAAUUGAGUGUA
..((((......))))..((((.((((((..........((((.....(((((.((((((((((.............)))))))))))))))..))))..........)))))).)))). (-29.78 = -29.72 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,685,115 – 4,685,223
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.47
Mean single sequence MFE -32.26
Consensus MFE -23.09
Energy contribution -23.65
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.88
Structure conservation index 0.72
SVM decision value 0.26
SVM RNA-class probability 0.657590
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4685115 108 - 22224390
UACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAGCUCCAAAUUACUGAGCUGAGCGAAUUUAAUUGCAUGUGAGCGACAU--UUCGCAG
...(((((......)))))-.(((((.....)))))((((((((..---------...((((((((((.........)))))..((((......))))..)))))...)))--))))).. ( -32.60)
>DroSec_CAF1 38739 108 - 1
UACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAGCUCCAAAUUACGGAGCUGAGCGAAUUUAAUUGGAUGUGAGCAACAU--UUCGCAG
...(((((......)))))-.(((((.....)))))((((((((..---------.......(((((((.......))))))).((..((((....))))....))..)))--))))).. ( -34.70)
>DroEre_CAF1 39135 108 - 1
UACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAACGCCAAAUUACUGAGCUGAGCAAAUUUAAUUGCAUGUGAGCGACAUCGUUCGU--
.(((..((((((.((..((-((((((......(((((.(((..(..---------..)))).))..)))........))))).)))..)).))))))..)))(((((....)))))..-- ( -27.04)
>DroYak_CAF1 35946 118 - 1
UACACUCAAUUACAUGAGUUUGGCUCCCUCCGGCCUGCGAAAUGGCAACUUUGGCAACUUCACAGCUCCAAAUUACUGAGCUGAGCGAAUUUAAUUGCAUGUGAGCGACAU--UUCGCAG
...(((((......)))))..((((......))))(((((((((((......(....)....((((((.........)))))).))........((((......)))))))--)))))). ( -34.70)
>consensus
UACACUCAAUUACAUGAGU_UGGCUCCCCCCGGGCUGCGAAAUGGA_________AACUUCACAGCUCCAAAUUACUGAGCUGAGCGAAUUUAAUUGCAUGUGAGCGACAU__UUCGCAG
((((..((((((.((..((.((((((.....((((((.(((.................))).)))).))........)))))).))..)).))))))..)))).((((......)))).. (-23.09 = -23.65 +   0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,685,153 – 4,685,263
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.61
Mean single sequence MFE -32.80
Consensus MFE -28.75
Energy contribution -28.87
Covariance contribution 0.12
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.88
SVM decision value 0.67
SVM RNA-class probability 0.816841
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4685153 110 + 22224390
CUCAGUAAUUUGGAGCUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUAAACUUGUCAGAGAAUUUAUUUAAUGCCUAAUCAAGUGAUG
(((......((((.((((((((((.---------...))))))))))))))((.(((...-(((((......))))).....))).)).)))...((((((.((.....)).)))))).. ( -28.70)
>DroSec_CAF1 38777 110 + 1
CUCCGUAAUUUGGAGCUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUAAACUUGUCAGAGCAUUUAUUUAAUGCCUAAUCAAGUGAUG
((((....(((((.((((((((((.---------...))))))))))))))).))))...-(((((......)))))....(((((..((.(((((.....)))))))...))))).... ( -36.60)
>DroEre_CAF1 39173 110 + 1
CUCAGUAAUUUGGCGUUGUGAAGUU---------UCCAUUUCGCAGCCCGGGGGGAGCCA-ACUCAUGUAAUUGAGUGUAAACUUGUCAGAGCAUUUAUUUAAUGCCUAAUCAAGUGAUG
..........((((((((((((((.---------...))))))))))((....)).))))-(((((......)))))....(((((..((.(((((.....)))))))...))))).... ( -32.10)
>DroYak_CAF1 35984 120 + 1
CUCAGUAAUUUGGAGCUGUGAAGUUGCCAAAGUUGCCAUUUCGCAGGCCGGAGGGAGCCAAACUCAUGUAAUUGAGUGUAAACUUGUCAGAGCAUUUAUUUAAUGCCUAAUCAAGUGAUG
(((.....(((((..(((((((((.((.......)).))))))))).)))))..)))....(((((......)))))....(((((..((.(((((.....)))))))...))))).... ( -33.80)
>consensus
CUCAGUAAUUUGGAGCUGUGAAGUU_________UCCAUUUCGCAGCCCGGGGGGAGCCA_ACUCAUGUAAUUGAGUGUAAACUUGUCAGAGCAUUUAUUUAAUGCCUAAUCAAGUGAUG
(((.....(((((.((((((((((.............)))))))))))))))..)))....(((((......)))))....(((((..((.(((((.....)))))))...))))).... (-28.75 = -28.87 +   0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,685,153 – 4,685,263
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.61
Mean single sequence MFE -26.96
Consensus MFE -20.25
Energy contribution -21.01
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.75
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4685153 110 - 22224390
CAUCACUUGAUUAGGCAUUAAAUAAAUUCUCUGACAAGUUUACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAGCUCCAAAUUACUGAG
....(((((.(((((.(((.....))).).))))))))).....((((.......(((.-...))).....((((((.(((..(..---------..)))).)))).)).......)))) ( -22.70)
>DroSec_CAF1 38777 110 - 1
CAUCACUUGAUUAGGCAUUAAAUAAAUGCUCUGACAAGUUUACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAGCUCCAAAUUACGGAG
....(((((.(((((((((.....))))).)))))))))...((((((......)))).-)).((((....((((((.(((..(..---------..)))).))))))........)))) ( -30.40)
>DroEre_CAF1 39173 110 - 1
CAUCACUUGAUUAGGCAUUAAAUAAAUGCUCUGACAAGUUUACACUCAAUUACAUGAGU-UGGCUCCCCCCGGGCUGCGAAAUGGA---------AACUUCACAACGCCAAAUUACUGAG
....(((((.(((((((((.....))))).))))))))).....((((......((.((-((((..((....))..))(((..(..---------..)))).))))..))......)))) ( -26.00)
>DroYak_CAF1 35984 120 - 1
CAUCACUUGAUUAGGCAUUAAAUAAAUGCUCUGACAAGUUUACACUCAAUUACAUGAGUUUGGCUCCCUCCGGCCUGCGAAAUGGCAACUUUGGCAACUUCACAGCUCCAAAUUACUGAG
....(((((.(((((((((.....))))).))))))))).....((((.......(((((.((((......))))(((.(((.(....)))).))).......)))))........)))) ( -28.76)
>consensus
CAUCACUUGAUUAGGCAUUAAAUAAAUGCUCUGACAAGUUUACACUCAAUUACAUGAGU_UGGCUCCCCCCGGGCUGCGAAAUGGA_________AACUUCACAGCUCCAAAUUACUGAG
....(((((.(((((((((.....))))).))))))))).....(((........(((.....))).....((((((.(((.................))).)))).))........))) (-20.25 = -21.01 +   0.75)

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 10:16:10 2006