Locus 4512

Sequence ID X_DroMel_CAF1
Location 11,909,949 – 11,910,109
Length 160
Max. P 0.993162
window7420 window7421

overview

Window 0

Location 11,909,949 – 11,910,046
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 67.31
Mean single sequence MFE -31.83
Consensus MFE -12.68
Energy contribution -13.10
Covariance contribution 0.42
Combinations/Pair 1.21
Mean z-score -1.75
Structure conservation index 0.40
SVM decision value 0.38
SVM RNA-class probability 0.713058
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11909949 97 + 22224390
---AAAA---------GUACAGCUCAAGUGGUGCAGGGGCGUUGCAAAAAGGGGAGCGUGGAAAGGGGAU----GGCGGUGGUGGUGCGGAUGGCAU-UGCCAUGUGCCG------GCUC
---....---------.(((.((((...(..(((((.....)))))..)....))))))).....(((.(----((((((((..((((.....))))-..)))).)))))------.))) ( -33.70)
>DroSec_CAF1 20387 94 + 1
AAAAAAA---------GUACAGCUCAAGUGGUGCAGGGGAGUUGCAAAAAGGGGAGCGGGGAAAGGGGCU----------GCUGGUGCGGAUGGCAU-UGCCAUGUGCCG------GCUC
.......---------.....((((...(..(((((.....)))))..)....)))).............----------(((((..(..(((((..-.))))))..)))------)).. ( -28.20)
>DroSim_CAF1 17899 94 + 1
AAAAAAA---------GUACAGCUCAAGUGGUGCAGGGGCGUUGCAAAAAGGGGAGCGGGGAAAGGGGCU----------GCUGGUGCGGAUGGCAU-UGCCAUGUGCCG------GCUC
.......---------....(((((..((..(((....)))..))......(....)........)))))----------(((((..(..(((((..-.))))))..)))------)).. ( -29.10)
>DroEre_CAF1 18316 76 + 1
---AAAA---------GUACAGCUCAAGUGGUGCAGGGGCGUUGCAAA------AAGGGGG-------------------AAUGGUGCGGAUGGCAU-AGCCAUGUGCCG------GCUC
---....---------((((..(((...(..(((((.....)))))..------)...)))-------------------....))))((.((((((-(....)))))))------.)). ( -21.30)
>DroYak_CAF1 21102 99 + 1
---AAAA---------GUACAGCUCAAGUGGUGCAGGGGGGGGGGGGA--GGCGAGGGGCGAAGGUAGGUGGUAGCCGGUGUUGGUGCGGAUGGCAU-UGCCAUUUGCCG------GCUC
---....---------((((.((....)).))))..............--......((((...(((((((((((((((.(((....)))..))))..-))))))))))).------)))) ( -30.30)
>DroAna_CAF1 40477 107 + 1
AGAAAAACUGAAACCCAUGAAGCUCAAGUGGUU----GGAGUUUCCA--GGGUGAGCCUUUAGUGGAGCC----UGC---CAUGUGCCAUGUGGCAUGUGGCAUGUGCCUGCUACGGCUC
............((((..(((((((........----.)))))))..--))))(((((..(((..(.(((----(((---((((((((....))))))))))).).)))..))).))))) ( -48.40)
>consensus
___AAAA_________GUACAGCUCAAGUGGUGCAGGGGCGUUGCAAA_AGGGGAGCGGGGAAAGGGGCU__________GAUGGUGCGGAUGGCAU_UGCCAUGUGCCG______GCUC
................((((.((....)).))))....................................................(((.(((((....))))).)))............ (-12.68 = -13.10 +   0.42)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,910,013 – 11,910,109
Length 96
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 86.18
Mean single sequence MFE -31.10
Consensus MFE -28.53
Energy contribution -28.77
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.23
Structure conservation index 0.92
SVM decision value 2.38
SVM RNA-class probability 0.993162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11910013 96 + 22224390
GGUGGUGCGGAUGGCAUUGCCAUGUGCCGGCUCCUUUGCACAUA----CAUACUGGUACAUAACUCAAAUAGCGACGCAGUUGUCUGCACCACCCCCCCA---
(((((((((((..((......(((((((((..............----....)))))))))..........((...)).))..)))))))))))......--- ( -37.37)
>DroSec_CAF1 20448 98 + 1
GCUGGUGCGGAUGGCAUUGCCAUGUGCCGGCUCCUUUGCACAUACAUACAUACUGGCACAUAACUCAAAUAGCGACGCAGUUGUCUGCACCACC--CCCA---
..(((((((((..((......(((((((((......((......))......)))))))))..........((...)).))..)))))))))..--....--- ( -34.30)
>DroSim_CAF1 17960 98 + 1
GCUGGUGCGGAUGGCAUUGCCAUGUGCCGGCUCCUUUGCACAUACAUACAUACUGGUACAUAACUCAAAUAGCGACGCAGUUGUCUGCACCACC--CCCA---
..(((((((((..((......(((((((((......((......))......)))))))))..........((...)).))..)))))))))..--....--- ( -32.30)
>DroEre_CAF1 18359 84 + 1
AAUGGUGCGGAUGGCAUAGCCAUGUGCCGGCUCCU-UGCAC--------AUACUGGUACAUAACUCAAAUAGCGACGCAGUUGUCUGCCCCCU----------
...((.(((((..((......(((((((((.....-.....--------...)))))))))..........((...)).))..)))))))...---------- ( -25.32)
>DroYak_CAF1 21168 93 + 1
GUUGGUGCGGAUGGCAUUGCCAUUUGCCGGCUCCUUUGCAC--------AUACUGGUACAUAACUCAAAUAGCGACGCAGUUGUCUGCACCCUC--CCCCUCC
...((((((((..((..(((((..((...((......)).)--------)...))))).............((...)).))..))))))))...--....... ( -26.20)
>consensus
GCUGGUGCGGAUGGCAUUGCCAUGUGCCGGCUCCUUUGCACAUA____CAUACUGGUACAUAACUCAAAUAGCGACGCAGUUGUCUGCACCACC__CCCA___
...((((((((..((......(((((((((......................)))))))))..........((...)).))..))))))))............ (-28.53 = -28.77 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:58 2006