Locus 378

Sequence ID 3R_DroMel_CAF1
Location 1,450,559 – 1,450,705
Length 146
Max. P 0.939882
window627 window628 window629

overview

Window 7

Location 1,450,559 – 1,450,665
Length 106
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 84.31
Mean single sequence MFE -29.82
Consensus MFE -24.16
Energy contribution -23.88
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -1.66
Structure conservation index 0.81
SVM decision value 0.16
SVM RNA-class probability 0.610950
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1450559 106 + 27905053
ACAGUGCUCGAGU-UGUU-UUCGUAUUAAACUUGAAUUUCCCUUUCAAUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGUCGCCUGGCCUCCGUGGUG
.(((.((((((((-(...-.........)))))))..................(((((..((....((((((....)))))).)).))))))))))(((.....))). ( -30.60)
>DroSec_CAF1 23143 106 + 1
ACUGUGCUCGAGU-UGUU-UUUGUAGUUAACUUGAAUUUCCCUUUAAAUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGCCGCCUGGCCUCCGUGGUG
((..((.((((((-((..-........)))))))).....((...........(((((((......)))))))((((((........))))))..))....))..)). ( -31.90)
>DroSim_CAF1 21463 106 + 1
ACAGUGCUCGAGU-UGUU-UUUGUAGUUAACUUGAAUUUCCCUUUAAAUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGCCGCCUGGCCUCCGUGGUG
.(((...((((((-((..-........))))))))..................(((((((......)))))))((((((........)))))))))(((.....))). ( -33.00)
>DroEre_CAF1 24675 104 + 1
ACAGUGCUCGAAU-UGUU-UUCUAAUUUAACUUAAAUUUU--UUUCCACUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGCCGCCUGGCCUCUGUGGUG
((((.(((.(((.-((..-....((((((...))))))..--....)).))).(((((((......)))))))((((((........))))))..)))..)))).... ( -29.60)
>DroYak_CAF1 23196 107 + 1
ACCGAAUCCGAAU-UGUUUUUCUUAUUUAACUUAAAUUUCCCUUUUAACUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGCCGCCUGGCCUCCGUGGUG
(((((((..(((.-.....)))..))))............((...........(((((((......)))))))((((((........))))))..)).......))). ( -26.40)
>DroAna_CAF1 24431 98 + 1
ACAA-ACUGGAUUCUGUU-UUAAUAAGAGACU--------CUUUUUUUUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGUUGGGCCGUCUGGCCUCCGUGGUC
..((-(..(((.(((.((-.....)).))).)--------))..)))......(((((((......)))))))((((((........))))))..((((.....)))) ( -27.40)
>consensus
ACAGUGCUCGAGU_UGUU_UUCGUAUUUAACUUGAAUUUCCCUUUAAAUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGCCGCCUGGCCUCCGUGGUG
.....................................................(((((((......)))))))((((((........))))))...(((.....))). (-24.16 = -23.88 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,450,593 – 1,450,705
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.70
Mean single sequence MFE -45.52
Consensus MFE -37.90
Energy contribution -36.93
Covariance contribution -0.97
Combinations/Pair 1.23
Mean z-score -2.47
Structure conservation index 0.83
SVM decision value 1.28
SVM RNA-class probability 0.939882
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1450593 112 + 27905053
UUUCCCUUU--------CAAUUUCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUCGGUCGCCUGGCCUCCGUGGUGGCCAAGUACCUGUUGCAGGGCGGCAAGGUGGCCGUGGUCC
....((...--------........(((((((......)))))))((((((((((.....(((((((((((.(....).))))..(((.....))).))))))).))))))))))))... ( -47.90)
>DroVir_CAF1 23702 117 + 1
UU-GUUUUUCUA--UUUAAUUUUUAGACCGUUGUUAUUGAUGGACGCGGCCAUUUGCUUGGCCGCCUGGCCUCCGUGGUUGCCAAGUACCUGUUGCAGGGCGGCAAGGUGGCCGUAGUCC
..-.....((((--.........))))..............(((((((((((......)))))))..((((.((...((((((..(((.....)))..))))))..)).))))...)))) ( -44.70)
>DroPse_CAF1 24941 104 + 1
--CCCC--------------UUGCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUGCUUGGCCGUCUGGCUUCCGUCGUCGCCAAGUACCUGUUGCAGGGCGGCAAGGUGGCCGUCGUUC
--....--------------.....(((((((......)))))))(((((((......)))))))..((((.((...((((((..(((.....)))..))))))..)).))))....... ( -44.20)
>DroGri_CAF1 23430 117 + 1
UUUGUCUUU--UUGCUU-GUCUGCAGACCGUUGUUAUUGAUGGUCGCGGCCAUUUACUGGGCCGCCUGGCCUCCGUUGUCGCCAAGUACCUGUUGCAGGGCGGCAAGGUAGCCGUGGUGC
.........--..((..-..(..(.(((((((......)))))))((((((........))))))..(((..((.((((((((..(((.....)))..))))))))))..))))..).)) ( -48.90)
>DroWil_CAF1 29012 109 + 1
UUUCA---U--------GUAUUGCAGACCGUUAUUAUUGAUGGACGCGGCCAUUUGCUGGGCCGUCUGGCCUCAGUUGUUGCCAAGUACCUGUUGCAGGGCGGCAAAGUGGCUGUGGUUC
.....---.--------..........((((((....)))))).(((((((((((((((((((....)))).))))(((((((..(((.....)))..)))))))))))))))))).... ( -45.30)
>DroMoj_CAF1 21823 110 + 1
UUUGUUUUU--A--------UUAUAGACCGUUGUUAUCGAUGGACGCGGCCAUUUGCUUGGCCGCCUGGCCUCCGUGGUAGCCAAGUACCUGUUGCAAGGCGGCAAGGUGGCUGUUGUGC
.........--.--------.......((((((....))))))(((((((((..((((((((..(((((...))).))..))))))))((((((((...))))).))))))))).))).. ( -42.10)
>consensus
UUUCUCUUU___________UUGCAGACCGUUGUUAUUGAUGGACGCGGCCAUUUGCUUGGCCGCCUGGCCUCCGUGGUCGCCAAGUACCUGUUGCAGGGCGGCAAGGUGGCCGUGGUCC
...........................((((((....))))))..((((((((((.....((((((((((..(....)..)))..(((.....))).))))))).))))))))))..... (-37.90 = -36.93 +  -0.97)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,450,593 – 1,450,705
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.70
Mean single sequence MFE -35.48
Consensus MFE -24.61
Energy contribution -25.17
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -1.96
Structure conservation index 0.69
SVM decision value 0.53
SVM RNA-class probability 0.773071
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1450593 112 - 27905053
GGACCACGGCCACCUUGCCGCCCUGCAACAGGUACUUGGCCACCACGGAGGCCAGGCGACCGAGCAAAUGGCCGCGACCAUCAAUAACAACGGUCUGAAAUUG--------AAAGGGAAA
...((.((((((..((((((.((((...))))..(((((((.(....).)))))))....)).)))).)))))).((((............))))........--------...)).... ( -38.50)
>DroVir_CAF1 23702 117 - 1
GGACUACGGCCACCUUGCCGCCCUGCAACAGGUACUUGGCAACCACGGAGGCCAGGCGGCCAAGCAAAUGGCCGCGUCCAUCAAUAACAACGGUCUAAAAAUUAAA--UAGAAAAAC-AA
((((...((((.((((((((.((((...))))....))))))....)).))))..(((((((......)))))))))))..............((((.........--)))).....-.. ( -40.90)
>DroPse_CAF1 24941 104 - 1
GAACGACGGCCACCUUGCCGCCCUGCAACAGGUACUUGGCGACGACGGAAGCCAGACGGCCAAGCAAAUGGCCGCGACCAUCAAUAACAACGGUCUGCAA--------------GGGG--
......((((......))))(((((((.........((((..(....)..))))(.((((((......)))))))((((............))))))).)--------------))).-- ( -35.40)
>DroGri_CAF1 23430 117 - 1
GCACCACGGCUACCUUGCCGCCCUGCAACAGGUACUUGGCGACAACGGAGGCCAGGCGGCCCAGUAAAUGGCCGCGACCAUCAAUAACAACGGUCUGCAGAC-AAGCAA--AAAGACAAA
((....((((......))))..(((((...(((.((((....))).)...)))..((((((........))))))((((............)))))))))..-..))..--......... ( -38.50)
>DroWil_CAF1 29012 109 - 1
GAACCACAGCCACUUUGCCGCCCUGCAACAGGUACUUGGCAACAACUGAGGCCAGACGGCCCAGCAAAUGGCCGCGUCCAUCAAUAAUAACGGUCUGCAAUAC--------A---UGAAA
......(((((...((((......))))..((.((.((((.....(((.((((....)))))))......)))).))))............)).)))......--------.---..... ( -28.00)
>DroMoj_CAF1 21823 110 - 1
GCACAACAGCCACCUUGCCGCCUUGCAACAGGUACUUGGCUACCACGGAGGCCAGGCGGCCAAGCAAAUGGCCGCGUCCAUCGAUAACAACGGUCUAUAA--------U--AAAAACAAA
.......(((((...((((...........))))..))))).......(((((..(((((((......)))))))(((....)))......)))))....--------.--......... ( -31.60)
>consensus
GAACCACGGCCACCUUGCCGCCCUGCAACAGGUACUUGGCAACCACGGAGGCCAGGCGGCCAAGCAAAUGGCCGCGACCAUCAAUAACAACGGUCUGCAA___________AAAGACAAA
.......(((((((((((......)))..))))..(((((..(....)..)))))((((((........))))))................))))......................... (-24.61 = -25.17 +   0.56)

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 09:41:48 2006