Locus 4405

Sequence ID 2L_DroMel_CAF1
Location 12,675,067 – 12,675,293
Length 226
Max. P 0.796874
window6940 window6941 window6942

overview

Window 0

Location 12,675,067 – 12,675,179
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.33
Mean single sequence MFE -30.60
Consensus MFE -24.38
Energy contribution -24.80
Covariance contribution 0.42
Combinations/Pair 1.09
Mean z-score -2.23
Structure conservation index 0.80
SVM decision value 0.06
SVM RNA-class probability 0.561354
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12675067 112 - 22407834
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCUCCUCUUCCUCUAUUGAUUUCCGUUGCUGAGGUUGCCUCAUCGAUUUGCGCUCGCUUUAAUCGGGUUCCUUUCUACU-----U---
((((((...((((.....((((((.((.....))))))))))))......))))))((....((((..(((....(((((.((....))...)))))))).))))...)).-----.--- ( -31.80)
>DroSec_CAF1 55740 113 - 1
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCUCCUCUUCCUCUAUUGAUUUCCGUUGCUGAGGUUUCCUCAUCGAUUUGCGCUCGGUUUAAUCGGGUUCCUUUCUACU----AU---
...((((((((((.....((((((.((.....))))))))..(((.(((((...(((.((((((((...))))).......)))..))).))))).))).)))))).))))----..--- ( -31.81)
>DroSim_CAF1 57628 113 - 1
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCUCCUCUUCCUCUAUUGAUUUCCGUUGCUGAGGUUUCCUCAUCGAUUUGCGCUCUCUUUAAUCGGGUUCCUUUCUACU----AU---
...((((((((((.....((((((.((.....))))))))..(((.(((((....(((((.(((((...))))).))....)))......))))).))).)))))).))))----..--- ( -27.60)
>DroEre_CAF1 57538 110 - 1
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCU---CUUCCUCUAUUGAUUUCCGUUGCUGAGGUUUCCUCAUCGAUUUGCGCUCGCUUUAAUCGGGUUCCUUUCUACU----AU---
...((((((((((((..(((((((.((.....)).---..))))))).))....((.....(((((...))))).(((((.((....))...))))))).)))))).))))----..--- ( -32.30)
>DroYak_CAF1 58316 110 - 1
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCU---CUUCCUCUAUUGAUUUCCGUUGCUGAGGUUUCCUCAUCGAUUUGCGCUCGCUUUAAUCGCGUUUCUUUCUACU----AC---
(((((.(((.(((.((((((((((.((.....)).---..)))))))..))).)))...(((((((...)))))..((((.((....))...)))))).))))))))....----..--- ( -29.80)
>DroAna_CAF1 48116 119 - 1
GGAAGUAAAAGGACAUUUGGAGGCUGCUUU-UGUCCUUUUUGCUCUAUUGAUUUCCGUUACUGAGGUUUCCUCAUCGAUUUGCACUCGCUUUAAUCGGGAACCUUCCUCUUUUUUAUUUC
(((((.(((((((((...((......))..-)))))))))............((((.....(((((...))))).(((((.((....))...))))))))).)))))............. ( -30.30)
>consensus
GGAAGUAAAAGGACAUUUAGAGGAUGCUUUGUGCUCCUCUUCCUCUAUUGAUUUCCGUUGCUGAGGUUUCCUCAUCGAUUUGCGCUCGCUUUAAUCGGGUUCCUUUCUACU____AU___
(((((.....(((.((((((((((.((.....))......)))))))..))).))).....(((((...)))))((((((.((....))...))))))....)))))............. (-24.38 = -24.80 +   0.42)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,675,179 – 12,675,293
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.03
Mean single sequence MFE -32.40
Consensus MFE -26.89
Energy contribution -27.95
Covariance contribution 1.06
Combinations/Pair 1.07
Mean z-score -2.18
Structure conservation index 0.83
SVM decision value 0.60
SVM RNA-class probability 0.796874
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12675179 114 + 22407834
GCAUUUGUAGCGCCGCAUCUU------CUGCCCCUCGUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCGCUGUCAAUCGGCGCUGCAAC
....(((((((((((.....(------(..(.....)..))................((((((..(((.(((((....)))))((((...))))...)))..))))))))))))))))). ( -35.80)
>DroSec_CAF1 55853 114 + 1
GCAUUUGUAGCGCCGCAUCUU------CUGCCCCUCGUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCGCUGACAAUCGGCGCUGCAAC
....(((((((((((.((..(------(.((....(((.(((.....))).)))......(((((....(((((....)))))((((...))))))))))).))..))))))))))))). ( -33.50)
>DroSim_CAF1 57741 120 + 1
GCAUUUGUAGCGCCGCAUCUUCUUCUUCUUCCCCUCUUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCGCUGACAAUCGGCGCUGCAAC
....(((((((((((((............(((......))).................(((....)))..))).((((((...((((...))))...))))))......)))))))))). ( -32.30)
>DroEre_CAF1 57648 114 + 1
GCAUUUGUAGCGCCGCAUAUU------CUGCCCUUCUUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCGCUGUCAAUCGGCGCUGCAAC
....(((((((((((......------....((.....)).................((((((..(((.(((((....)))))((((...))))...)))..))))))))))))))))). ( -34.50)
>DroYak_CAF1 58426 114 + 1
GCAUUUGUAGCGCCGCAUCUU------CUGCCCUUCCAGGAUUAUUUAUUAACGUUUAUUGAUUCCGACUUGCCCGGCGGCAAUCUGCCACAGAAAAUCGCUGUCAAACGGCGCUGCAAC
....(((((((((((....((------(((......))))).................(((((..(((.(((((....)))))((((...))))...)))..))))).))))))))))). ( -36.10)
>DroAna_CAF1 48235 111 + 1
GCAUUCGUGGAGCAGCAUCUU---------CCCUUCUUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCUUUGUCAUCCGCUACUGCAAC
(((...(((((((((.....(---------((......)))............................(((((....))))).)))).(((((.....)))))..)))))...)))... ( -22.20)
>consensus
GCAUUUGUAGCGCCGCAUCUU______CUGCCCCUCUUGGAUUAUUUAUUAACGUUUAUUGAUUUCGACUUGCCCAGCGGCAAUCUGCCACAGAAAAUCGCUGUCAAUCGGCGCUGCAAC
....(((((((((((................((.....))..................(((((..(((.(((((....)))))((((...))))...)))..))))).))))))))))). (-26.89 = -27.95 +   1.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,675,179 – 12,675,293
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.03
Mean single sequence MFE -34.17
Consensus MFE -28.92
Energy contribution -30.33
Covariance contribution 1.42
Combinations/Pair 1.06
Mean z-score -1.55
Structure conservation index 0.85
SVM decision value -0.03
SVM RNA-class probability 0.519278
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12675179 114 - 22407834
GUUGCAGCGCCGAUUGACAGCGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCACGAGGGGCAG------AAGAUGCGGCGCUACAAAUGC
.(((.((((((.(((((...((((((((((((((.....))))).))).))))))...)))))................(((....)))(((.------....))))))))).))).... ( -36.70)
>DroSec_CAF1 55853 114 - 1
GUUGCAGCGCCGAUUGUCAGCGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCACGAGGGGCAG------AAGAUGCGGCGCUACAAAUGC
.(((.((((((.((((....((((((((((((((.....))))).))).))))))....))))................(((....)))(((.------....))))))))).))).... ( -35.40)
>DroSim_CAF1 57741 120 - 1
GUUGCAGCGCCGAUUGUCAGCGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCAAGAGGGGAAGAAGAAGAAGAUGCGGCGCUACAAAUGC
.(((.(((((((((((....((((((((((((((.....))))).))).))))))....))))................(((......)))..............))))))).))).... ( -35.80)
>DroEre_CAF1 57648 114 - 1
GUUGCAGCGCCGAUUGACAGCGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCAAGAAGGGCAG------AAUAUGCGGCGCUACAAAUGC
.(((.((((((.(((((...((((((((((((((.....))))).))).))))))...))))).................((.....))(((.------....))))))))).))).... ( -36.00)
>DroYak_CAF1 58426 114 - 1
GUUGCAGCGCCGUUUGACAGCGAUUUUCUGUGGCAGAUUGCCGCCGGGCAAGUCGGAAUCAAUAAACGUUAAUAAAUAAUCCUGGAAGGGCAG------AAGAUGCGGCGCUACAAAUGC
.(((.((((((((((((...((((((((((((((.....)))).)))).))))))...))))...................(((......)))------.....)))))))).))).... ( -34.90)
>DroAna_CAF1 48235 111 - 1
GUUGCAGUAGCGGAUGACAAAGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCAAGAAGGG---------AAGAUGCUGCUCCACGAAUGC
((.(.(((((((..(((....(((((((((((((.....))))).))).)))))....)))..................(((......))---------)...)))))))).))...... ( -26.20)
>consensus
GUUGCAGCGCCGAUUGACAGCGAUUUUCUGUGGCAGAUUGCCGCUGGGCAAGUCGAAAUCAAUAAACGUUAAUAAAUAAUCCAAGAAGGGCAG______AAGAUGCGGCGCUACAAAUGC
.(((.((((((((((((...((((((((((((((.....))))).))).))))))...)))))................(((.....)))...............))))))).))).... (-28.92 = -30.33 +   1.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:06 2006