Locus 1663

Sequence ID 3L_DroMel_CAF1
Location 4,824,001 – 4,824,101
Length 100
Max. P 0.930363
window2573 window2574

overview

Window 3

Location 4,824,001 – 4,824,101
Length 100
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 77.06
Mean single sequence MFE -28.10
Consensus MFE -18.85
Energy contribution -19.10
Covariance contribution 0.25
Combinations/Pair 1.17
Mean z-score -1.78
Structure conservation index 0.67
SVM decision value 1.18
SVM RNA-class probability 0.926356
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4824001 100 + 23771897
AGGGGCGGUC-CCAGUUACCGCCCAUAGGAAAUAUAACUCCUCAACUUUUGUCAGCCAUACUGAGGAAAAA--UGAAGAGCAAAGUUGCUGAGGAAA------------AAAAGU
..(((((((.-......)))))))..............(((((...((((.((((.....)))).))))..--.....((((....)))))))))..------------...... ( -30.30)
>DroSec_CAF1 51574 102 + 1
AGGGGCGGUCCCCAGUUACCGCCCAUAGGAAAUAUAACUCCUCAACUUUUGUCAGCCAUACUGAGGGAAAA--UGGAAAGCAAAGUUGGUGGGGAAA-----------AAAAAGU
..(((((((........))))))).............((((((((((((.((...((((...........)--)))...)))))))))).))))...-----------....... ( -31.00)
>DroSim_CAF1 54025 99 + 1
AGGGGCGGUC-CCAGUUACCGCCCAUAGGAAAUAUAACUCCUCAACUUUUGUCAGCCAUACUGAGGGAAAA--UGGAAAGCAAAAUUGCAGAGGAAA-------------AAGGU
..(((((((.-......)))))))..............(((((...((((.((((.....)))).))))..--......(((....))).)))))..-------------..... ( -29.30)
>DroEre_CAF1 52468 93 + 1
AGGGGCGGUC-CCGGUUACCGCCCAUAGGAAAUAUAACUCUUCAACUUUUG----CUAUACUGAGGGAAAA--UGGAUAACAGAGUUGCUGAAA---------------GAAGGU
..(((((((.-......)))))))..........(((((((((...((((.----((......)).)))).--..))....)))))))......---------------...... ( -22.30)
>DroYak_CAF1 52450 99 + 1
AGGGGCGGUC-CUGGUUACCGCCCAUAGGAAAUAUAACUCUUCAACUUUUGUCAGCCAUACUGAGGGAAAA--UGGAAGGCAGAGUGGCCAAAAAA-------------AAAUGU
..(((((((.-......)))))))................((((..((((.((((.....)))).))))..--)))).(((......)))......-------------...... ( -26.20)
>DroAna_CAF1 56139 110 + 1
AGGGGCGGGC-CUGGUUGCCGCCCAUAGGAAAUAUAACUCCACAACUUUUGCCAGCUCUACUGGGGGAAAUAAUAGGGA----UUAUACGGGGGAAUGUAUAUCUAAUAACGAGC
..((((((..-.......))))))...(((.(((((.((((.....((((.((((.....)))).))))(((((....)----))))..))))...))))).))).......... ( -29.50)
>consensus
AGGGGCGGUC_CCAGUUACCGCCCAUAGGAAAUAUAACUCCUCAACUUUUGUCAGCCAUACUGAGGGAAAA__UGGAAAGCAAAGUUGCUGAGGAAA____________AAAAGU
..(((((((........)))))))...(((........))).....((((.((((.....)))).)))).............................................. (-18.85 = -19.10 +   0.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,824,001 – 4,824,101
Length 100
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 77.06
Mean single sequence MFE -25.64
Consensus MFE -17.56
Energy contribution -18.48
Covariance contribution 0.92
Combinations/Pair 1.29
Mean z-score -1.76
Structure conservation index 0.68
SVM decision value 1.20
SVM RNA-class probability 0.930363
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4824001 100 - 23771897
ACUUUU------------UUUCCUCAGCAACUUUGCUCUUCA--UUUUUCCUCAGUAUGGCUGACAAAAGUUGAGGAGUUAUAUUUCCUAUGGGCGGUAACUGG-GACCGCCCCU
......------------................((((((((--.((((..((((.....))))..)))).))))))))............(((((((......-.))))))).. ( -29.30)
>DroSec_CAF1 51574 102 - 1
ACUUUUU-----------UUUCCCCACCAACUUUGCUUUCCA--UUUUCCCUCAGUAUGGCUGACAAAAGUUGAGGAGUUAUAUUUCCUAUGGGCGGUAACUGGGGACCGCCCCU
.......-----------.........(((((((.....(((--(...........))))......)))))))(((((......)))))..(((((((........))))))).. ( -26.90)
>DroSim_CAF1 54025 99 - 1
ACCUU-------------UUUCCUCUGCAAUUUUGCUUUCCA--UUUUCCCUCAGUAUGGCUGACAAAAGUUGAGGAGUUAUAUUUCCUAUGGGCGGUAACUGG-GACCGCCCCU
.....-------------.((((((.((..((((((...(((--(...........))))..).))))))).)))))).............(((((((......-.))))))).. ( -26.10)
>DroEre_CAF1 52468 93 - 1
ACCUUC---------------UUUCAGCAACUCUGUUAUCCA--UUUUCCCUCAGUAUAG----CAAAAGUUGAAGAGUUAUAUUUCCUAUGGGCGGUAACCGG-GACCGCCCCU
......---------------.(((..(((((.((((((.(.--..........).))))----))..)))))..))).............(((((((......-.))))))).. ( -21.20)
>DroYak_CAF1 52450 99 - 1
ACAUUU-------------UUUUUUGGCCACUCUGCCUUCCA--UUUUCCCUCAGUAUGGCUGACAAAAGUUGAAGAGUUAUAUUUCCUAUGGGCGGUAACCAG-GACCGCCCCU
.((.((-------------(((.(..((((..(((.......--........)))..))))..).))))).))..................(((((((......-.))))))).. ( -26.16)
>DroAna_CAF1 56139 110 - 1
GCUCGUUAUUAGAUAUACAUUCCCCCGUAUAA----UCCCUAUUAUUUCCCCCAGUAGAGCUGGCAAAAGUUGUGGAGUUAUAUUUCCUAUGGGCGGCAACCAG-GCCCGCCCCU
..........................((((((----..((.((.((((...((((.....))))...)))).))))..)))))).......(((((((......-).)))))).. ( -24.20)
>consensus
ACUUUU____________UUUCCUCAGCAACUUUGCUUUCCA__UUUUCCCUCAGUAUGGCUGACAAAAGUUGAGGAGUUAUAUUUCCUAUGGGCGGUAACCGG_GACCGCCCCU
...................(((((((((......(.....)..........((((.....)))).....))))))))).............(((((((........))))))).. (-17.56 = -18.48 +   0.92)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:13 2006