Locus 542

Sequence ID 3L_DroMel_CAF1
Location 1,571,972 – 1,572,107
Length 135
Max. P 0.998543
window825 window826 window827 window828

overview

Window 5

Location 1,571,972 – 1,572,068
Length 96
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.78
Mean single sequence MFE -33.42
Consensus MFE -22.53
Energy contribution -22.81
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.67
SVM decision value 1.28
SVM RNA-class probability 0.939196
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1571972 96 + 23771897
UCGCCU-------UUUGGCCUGGCCAAGUGUAGUAAGUAAGUAAGUAG----------------UUGGCUGAAUGAAGAGCCACGUGCAGUGGUUCUCAGUGGCUGCCAGUGGUGGCCA
..(((.-------...)))..((((((.((...((......))..)).----------------))))))...(((.(((((((.....)))))))))).((((..((...))..)))) ( -35.00)
>DroSec_CAF1 16456 78 + 1
UCGCCU-------UUUGGCCUGGCCAAGUGCAGUA--------AGUAG----------------UUGGCUGAAUGAAGAGCCAAGUGCAGUGGUUCUCAC----------UGGUGGCCA
..(((.-------...)))..(((((.........--------.(((.----------------((((((........)))))).)))((((.....)))----------)..))))). ( -29.10)
>DroSim_CAF1 16639 78 + 1
UCGCCU-------UUUGGCCUGGCCAAGUGCAGUA--------AGUAG----------------UUGGCUGAAUGUAGAGCCACGUGCAGUGGUUCUCAC----------UGGUGGCCA
......-------..(((((.((((((.(((....--------.))).----------------))))))...((.((((((((.....)))))))))).----------....))))) ( -33.20)
>DroEre_CAF1 22754 101 + 1
UCGUCU-------UUUGGCCUGGCCAAGUGCAGUA--------AGUGGUUGUUUGGGCCGAAUGUUGGCUGAGUGAAGAGCCACGUGCAGUGCUUCUCAGUGGCUGCCA---GUGGCCA
..(((.-------.(((((..(((((((..(.(((--------.((((((.((((((((((...))))))...)))).)))))).))).)..))......)))))))))---).))).. ( -37.10)
>DroYak_CAF1 17183 96 + 1
UCGCCUUUUAGCUUUUGGCCUGGCCAAGUGCAGUA--------AGUAGUU------------UGUUGGCUGAAUGAAGAGCCACGUGCAGUGGUUCCCAGUGGCUGUCA---GUGGCCA
..(((...(((((.((((...(((((...((((..--------......)------------)))))))).......(((((((.....))))))))))).)))))...---..))).. ( -32.70)
>consensus
UCGCCU_______UUUGGCCUGGCCAAGUGCAGUA________AGUAG________________UUGGCUGAAUGAAGAGCCACGUGCAGUGGUUCUCAGUGGCUG_CA_UGGUGGCCA
..(((...........)))..(((((....((((.................................))))..((.((((((((.....))))))))))..............))))). (-22.53 = -22.81 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,571,972 – 1,572,068
Length 96
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 75.78
Mean single sequence MFE -26.30
Consensus MFE -18.37
Energy contribution -18.61
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.70
SVM decision value 1.90
SVM RNA-class probability 0.981879
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1571972 96 - 23771897
UGGCCACCACUGGCAGCCACUGAGAACCACUGCACGUGGCUCUUCAUUCAGCCAA----------------CUACUUACUUACUUACUACACUUGGCCAGGCCAAA-------AGGCGA
((((((....((((((((((((((.....)).)).)))))).........)))).----------------.....((......)).......)))))).(((...-------.))).. ( -24.30)
>DroSec_CAF1 16456 78 - 1
UGGCCACCA----------GUGAGAACCACUGCACUUGGCUCUUCAUUCAGCCAA----------------CUACU--------UACUGCACUUGGCCAGGCCAAA-------AGGCGA
((((((.((----------(((.....)))))...((((((........))))))----------------.....--------.........)))))).(((...-------.))).. ( -25.90)
>DroSim_CAF1 16639 78 - 1
UGGCCACCA----------GUGAGAACCACUGCACGUGGCUCUACAUUCAGCCAA----------------CUACU--------UACUGCACUUGGCCAGGCCAAA-------AGGCGA
((((((.((----------(((((....((.....))((((........))))..----------------...))--------)))))....)))))).(((...-------.))).. ( -26.10)
>DroEre_CAF1 22754 101 - 1
UGGCCAC---UGGCAGCCACUGAGAAGCACUGCACGUGGCUCUUCACUCAGCCAACAUUCGGCCCAAACAACCACU--------UACUGCACUUGGCCAGGCCAAA-------AGACGA
(((((..---((((((((((((((.....)).)).)))))).........))))......((((............--------..........)))).)))))..-------...... ( -28.75)
>DroYak_CAF1 17183 96 - 1
UGGCCAC---UGACAGCCACUGGGAACCACUGCACGUGGCUCUUCAUUCAGCCAACA------------AACUACU--------UACUGCACUUGGCCAGGCCAAAAGCUAAAAGGCGA
(((((..---(((.((((((((.(......).)).))))))..)))....(((((..------------.......--------........)))))..)))))...(((....))).. ( -26.43)
>consensus
UGGCCACCA_UG_CAGCCACUGAGAACCACUGCACGUGGCUCUUCAUUCAGCCAA________________CUACU________UACUGCACUUGGCCAGGCCAAA_______AGGCGA
(((((...............(((((.((((.....)))).))).))....(((((.....................................)))))..)))))............... (-18.37 = -18.61 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,572,005 – 1,572,107
Length 102
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 72.74
Mean single sequence MFE -35.10
Consensus MFE -22.73
Energy contribution -23.22
Covariance contribution 0.50
Combinations/Pair 1.05
Mean z-score -2.40
Structure conservation index 0.65
SVM decision value 3.14
SVM RNA-class probability 0.998543
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1572005 102 + 23771897
GUAAGUAG----------------UUGGCUGAAUGAAGAGCCACGUGCAGUGGUUCUCAGUGGCUGCCAGUGGUGGCCAACGAGCCAGCUAGCCACCCCAAACACCCAAUCCAUCCA-A
.....(((----------------((((((...(((.(((((((.....)))))))))).((((..((...))..))))...)))))))))..........................-. ( -38.30)
>DroSec_CAF1 16484 82 + 1
---AGUAG----------------UUGGCUGAAUGAAGAGCCAAGUGCAGUGGUUCUCAC----------UGGUGGCCAACGAGCCGGCAAGCCACCCAAAACACCCAAUC--------
---.(((.----------------((((((........)))))).))).((((((.....----------((.((((......)))).))))))))...............-------- ( -26.20)
>DroSim_CAF1 16667 89 + 1
---AGUAG----------------UUGGCUGAAUGUAGAGCCACGUGCAGUGGUUCUCAC----------UGGUGGCCAACGAGCCAGCAAGCCACCCAAAACACCCAAUCCAUCCA-A
---....(----------------((((.((..((.((((((((.....)))))))))).----------.((((((...(......)...)))))).....)).))))).......-. ( -28.30)
>DroEre_CAF1 22782 113 + 1
---AGUGGUUGUUUGGGCCGAAUGUUGGCUGAGUGAAGAGCCACGUGCAGUGCUUCUCAGUGGCUGCCA---GUGGCCAACGGGCCGCCAAGCCACUCAAACCAUCCAAACCACCCAAA
---.(((((((..((((((((...)))))((((((...((((((.((.((.....))))))))))((..---((((((....))))))...))))))))..)))..).))))))..... ( -47.60)
>consensus
___AGUAG________________UUGGCUGAAUGAAGAGCCACGUGCAGUGGUUCUCAC__________UGGUGGCCAACGAGCCAGCAAGCCACCCAAAACACCCAAUCCAUCCA_A
.........................(((((...((.((((((((.....))))))))))............(.((((......)))).).)))))........................ (-22.73 = -23.22 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,572,005 – 1,572,107
Length 102
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 72.74
Mean single sequence MFE -37.58
Consensus MFE -23.20
Energy contribution -25.20
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 0.62
SVM decision value 2.00
SVM RNA-class probability 0.985150
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1572005 102 - 23771897
U-UGGAUGGAUUGGGUGUUUGGGGUGGCUAGCUGGCUCGUUGGCCACCACUGGCAGCCACUGAGAACCACUGCACGUGGCUCUUCAUUCAGCCAA----------------CUACUUAC
(-(((.((((((((.((((...((((((((((......))))))))))...)))).)))..((((.((((.....)))).)))).))))).))))----------------........ ( -41.70)
>DroSec_CAF1 16484 82 - 1
--------GAUUGGGUGUUUUGGGUGGCUUGCCGGCUCGUUGGCCACCA----------GUGAGAACCACUGCACUUGGCUCUUCAUUCAGCCAA----------------CUACU---
--------...(((((((....(((((((.((......)).)))))))(----------(((.....))))))))((((((........))))))----------------)))..--- ( -27.30)
>DroSim_CAF1 16667 89 - 1
U-UGGAUGGAUUGGGUGUUUUGGGUGGCUUGCUGGCUCGUUGGCCACCA----------GUGAGAACCACUGCACGUGGCUCUACAUUCAGCCAA----------------CUACU---
.-(((.(((.((((((((....(((((((.((......)).))))))).----------...(((.((((.....)))).)))))))))))))).----------------)))..--- ( -34.20)
>DroEre_CAF1 22782 113 - 1
UUUGGGUGGUUUGGAUGGUUUGAGUGGCUUGGCGGCCCGUUGGCCAC---UGGCAGCCACUGAGAAGCACUGCACGUGGCUCUUCACUCAGCCAACAUUCGGCCCAAACAACCACU---
(((((((.(..((..(((((.((((((((.((.((((....)))).)---))))((((((((((.....)).)).))))))...)))))))))).))..).)))))))........--- ( -47.10)
>consensus
U_UGGAUGGAUUGGGUGUUUUGGGUGGCUUGCCGGCUCGUUGGCCACCA__________CUGAGAACCACUGCACGUGGCUCUUCAUUCAGCCAA________________CUACU___
......(((.(((((((.....(((((((.((......)).))))))).............((((.((((.....)))).))))))))))))))......................... (-23.20 = -25.20 +   2.00)

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 09:44:52 2006