Locus 8297

Sequence ID X_DroMel_CAF1
Location 20,629,516 – 20,629,629
Length 113
Max. P 0.986044
window13622 window13623

overview

Window 2

Location 20,629,516 – 20,629,629
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.98
Mean single sequence MFE -39.10
Consensus MFE -34.11
Energy contribution -35.67
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.87
SVM decision value 1.19
SVM RNA-class probability 0.928418
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20629516 113 + 22224390
---AAGGGAAAACUCCAUGUGGAGCGGCAGUACGUGCGAGUUCAGUUACCUGAACGGACUGGGAAAUGCUGGGAAAUUCAGCGAAACCCUGCGGAUAUUGGAGCAAGUGCUGCCAC----
---.........((((....)))).((((((((.(((..((((((....)))))).....(((...((((((.....))))))...))).............))).))))))))..---- ( -42.20)
>DroSec_CAF1 33638 101 + 1
---AAGGGG--ACUCCAUGUGGGGCGGCAGUACGUGCGAGUUCAGUUACCUGAACGGACUGGG----------AAAUUCAGCGAAACCCUGCGGUUAUUGGAGCAAGUGCUGCCAC----
---.....(--.((((....)))))((((((((.(((..((((((....))))))........----------...(((((...((((....)))).)))))))).))))))))..---- ( -35.40)
>DroEre_CAF1 33679 113 + 1
---AGGGGAAAACUCAAUGUGGGGCGGCAGUACGUGCGAGUUCAGUUACCUGAACGGACUGGGAAAUGCUGGGAAAUUCAGCGAAACCCUGCGGAUAUUGGUGCAAGUGCUGCCAA----
---.(((.....)))..........((((((((.((((.((((((....)))))).....(((...((((((.....))))))...)))............)))).))))))))..---- ( -39.60)
>DroYak_CAF1 34545 120 + 1
CGAAGGGAAAAACUCAAAGUGGGGCGGCAGUACGUGCGAGUUCAGUUACCUGAACGAACUGGGAAAUGCUUGGAAAUUCAGCGAAACCCUGCGGAUAUUGGAGCAGGUGCUGCCGAAUUG
............(((.....))).(((((((((.(((..((((((....)))))).....(((...((((.((....))))))...))).............))).)))))))))..... ( -39.20)
>consensus
___AAGGGAAAACUCAAUGUGGGGCGGCAGUACGUGCGAGUUCAGUUACCUGAACGGACUGGGAAAUGCUGGGAAAUUCAGCGAAACCCUGCGGAUAUUGGAGCAAGUGCUGCCAA____
............(((......))).((((((((.(((..((((((....)))))).....(((...((((((.....))))))...))).............))).))))))))...... (-34.11 = -35.67 +   1.56)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 20,629,516 – 20,629,629
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.98
Mean single sequence MFE -33.92
Consensus MFE -29.54
Energy contribution -31.10
Covariance contribution 1.56
Combinations/Pair 1.04
Mean z-score -2.49
Structure conservation index 0.87
SVM decision value 2.03
SVM RNA-class probability 0.986044
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20629516 113 - 22224390
----GUGGCAGCACUUGCUCCAAUAUCCGCAGGGUUUCGCUGAAUUUCCCAGCAUUUCCCAGUCCGUUCAGGUAACUGAACUCGCACGUACUGCCGCUCCACAUGGAGUUUUCCCUU---
----..(((((.((.(((.............(((....((((.......))))....))).....((((((....))))))..))).)).)))))(((((....)))))........--- ( -39.50)
>DroSec_CAF1 33638 101 - 1
----GUGGCAGCACUUGCUCCAAUAACCGCAGGGUUUCGCUGAAUUU----------CCCAGUCCGUUCAGGUAACUGAACUCGCACGUACUGCCGCCCCACAUGGAGU--CCCCUU---
----(((((((.((.(((.............(((.(((...)))...----------))).....((((((....))))))..))).)).))))))).((....))...--......--- ( -31.00)
>DroEre_CAF1 33679 113 - 1
----UUGGCAGCACUUGCACCAAUAUCCGCAGGGUUUCGCUGAAUUUCCCAGCAUUUCCCAGUCCGUUCAGGUAACUGAACUCGCACGUACUGCCGCCCCACAUUGAGUUUUCCCCU---
----..(((((.((.(((.............(((....((((.......))))....))).....((((((....))))))..))).)).)))))......................--- ( -33.60)
>DroYak_CAF1 34545 120 - 1
CAAUUCGGCAGCACCUGCUCCAAUAUCCGCAGGGUUUCGCUGAAUUUCCAAGCAUUUCCCAGUUCGUUCAGGUAACUGAACUCGCACGUACUGCCGCCCCACUUUGAGUUUUUCCCUUCG
.....((((((.((.(((.............(((....(((.........)))....))).....((((((....))))))..))).)).))))))........................ ( -31.60)
>consensus
____GUGGCAGCACUUGCUCCAAUAUCCGCAGGGUUUCGCUGAAUUUCCCAGCAUUUCCCAGUCCGUUCAGGUAACUGAACUCGCACGUACUGCCGCCCCACAUGGAGUUUUCCCCU___
....(((((((.((.(((.............(((....((((.......))))....))).....((((((....))))))..))).)).)))))))....................... (-29.54 = -31.10 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:25 2006