Locus 9669

Sequence ID 3R_DroMel_CAF1
Location 25,567,101 – 25,567,236
Length 135
Max. P 0.987035
window15451 window15452 window15453 window15454

overview

Window 1

Location 25,567,101 – 25,567,207
Length 106
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.85
Mean single sequence MFE -29.15
Consensus MFE -20.51
Energy contribution -20.90
Covariance contribution 0.39
Combinations/Pair 1.20
Mean z-score -2.69
Structure conservation index 0.70
SVM decision value 1.24
SVM RNA-class probability 0.935214
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25567101 106 + 27905053
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAGUCCAAGCUUUGAGUGGGAGCACC--CCAUCUCAAAGUU-A---CAAAUGCGCGAAGCGCAAUGCAAC-AA--AA
...((((.....(((....(((.((....)).))).....)))..(((((((((((((.....)--))).)))))))))-.---....(((((...)))))..)))).-..--.. ( -31.30)
>DroVir_CAF1 59206 101 + 1
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAAUCCAAGCUUUAG-AUCAUCCAAU--CUAUCU-AAAGCA-------ACUGCGCGAGGCGCAAUGUAAAA-C--CA
(((.((((((.((.((...(((.((....)).)))...........(((((((-((........--..))))-))))).-------..)))).)))))).)))......-.--.. ( -24.10)
>DroPse_CAF1 49045 106 + 1
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAAUCCAAGCUUUGAGUUGAUC-CCU--CAACCUCAAGGCU-G---CAACUGCGCGAGGCGCAAUGUAAAGCA--AA
.....(((((.((.((...(((.((....)).)))..........(((((((((((((..-..)--))).)))))))))-.---....)))).)))))((........)).--.. ( -30.30)
>DroGri_CAF1 60967 107 + 1
AAUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAAUCCAAGCUUUAGGAUAAUC--CU--CAACCU-AAAGCU-ACACAAACUGCGCGAGGCGCAAUGUAAACAA--CA
.....(((((.((.((...(((.((....)).)))..........(((((((((......--..--...)))-))))))-........)))).))))).............--.. ( -25.40)
>DroAna_CAF1 60261 111 + 1
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAGUCCAAGCUUUGAGUGAGAUUACCACUCAUCUCAAGGCUGA---AAAGUGCGCGAGGCGCAAUGCAGA-AUAUCA
(((((((.....(((....(((.((....)).))).....)))..(((((((((((((.......)))).)))))))))..---....(((((...)))))..)))))-)).... ( -33.50)
>DroPer_CAF1 48090 106 + 1
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAAUCCAAGCUUUGAGUUGAUC-CCU--CAACCUCAAGGCU-G---CAACUGCGCGAGGCGCAAUGUAAAGCA--AA
.....(((((.((.((...(((.((....)).)))..........(((((((((((((..-..)--))).)))))))))-.---....)))).)))))((........)).--.. ( -30.30)
>consensus
AUUUUGCCUCUUGACAAUUAGCCGCCAACGCUGCUCCAAAAUCCAAGCUUUGAGUUGAUC_ACU__CAACCUCAAAGCU_A___CAACUGCGCGAGGCGCAAUGUAAA_AA__AA
.....(((((.((.((...(((.((....)).)))...........(((((((((((.........))).))))))))..........)))).)))))................. (-20.51 = -20.90 +   0.39)

alignment

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secondary structure

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dotplot

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Window 2

Location 25,567,101 – 25,567,207
Length 106
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.85
Mean single sequence MFE -34.03
Consensus MFE -21.76
Energy contribution -22.46
Covariance contribution 0.69
Combinations/Pair 1.04
Mean z-score -1.66
Structure conservation index 0.64
SVM decision value 0.22
SVM RNA-class probability 0.638216
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25567101 106 - 27905053
UU--UU-GUUGCAUUGCGCUUCGCGCAUUUG---U-AACUUUGAGAUGG--GGUGCUCCCACUCAAAGCUUGGACUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
..--..-((((((.(((((...)))))..))---)-)))((((((.(((--(.....))))))))))((((.(((.....(((.((....)).)))....)))...))))..... ( -37.30)
>DroVir_CAF1 59206 101 - 1
UG--G-UUUUACAUUGCGCCUCGCGCAGU-------UGCUUU-AGAUAG--AUUGGAUGAU-CUAAAGCUUGGAUUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
..--.-...........(((((..((.((-------((((((-((((((--(((....)))-)))..........)))))))))))....))(((.....)))..)))))..... ( -30.00)
>DroPse_CAF1 49045 106 - 1
UU--UGCUUUACAUUGCGCCUCGCGCAGUUG---C-AGCCUUGAGGUUG--AGG-GAUCAACUCAAAGCUUGGAUUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
..--.((........))(((((..(((((((---(-.((((((((.(((--(..-..))))))))).((((.(....).))))......))).)).))))))...)))))..... ( -35.90)
>DroGri_CAF1 60967 107 - 1
UG--UUGUUUACAUUGCGCCUCGCGCAGUUUGUGU-AGCUUU-AGGUUG--AG--GAUUAUCCUAAAGCUUGGAUUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAUU
.(--((((..((.((((.((..((((.....))))-((((((-(((.((--(.--..))).)))))))))........)).)))).))..)))))...(((((....)))))... ( -32.00)
>DroAna_CAF1 60261 111 - 1
UGAUAU-UCUGCAUUGCGCCUCGCGCACUUU---UCAGCCUUGAGAUGAGUGGUAAUCUCACUCAAAGCUUGGACUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
......-..........(((((((((.((.(---(((((.(((((.((((.......))))))))).)).))))....)).)).)).(((((((....))))))))))))..... ( -33.10)
>DroPer_CAF1 48090 106 - 1
UU--UGCUUUACAUUGCGCCUCGCGCAGUUG---C-AGCCUUGAGGUUG--AGG-GAUCAACUCAAAGCUUGGAUUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
..--.((........))(((((..(((((((---(-.((((((((.(((--(..-..))))))))).((((.(....).))))......))).)).))))))...)))))..... ( -35.90)
>consensus
UG__UU_UUUACAUUGCGCCUCGCGCAGUUG___U_AGCCUUGAGAUUG__AGU_GAUCAACUCAAAGCUUGGAUUUUGGAGCAGCGUUGGCGGCUAAUUGUCAAGAGGCAAAAU
.................(((((((((..............(((((................))))).((((.(....).)))).))))((((((....)))))).)))))..... (-21.76 = -22.46 +   0.69)

alignment

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secondary structure

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dotplot

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Window 3

Location 25,567,141 – 25,567,236
Length 95
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 74.69
Mean single sequence MFE -26.05
Consensus MFE -24.97
Energy contribution -23.72
Covariance contribution -1.25
Combinations/Pair 1.27
Mean z-score -3.66
Structure conservation index 0.96
SVM decision value 1.35
SVM RNA-class probability 0.945014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25567141 95 + 27905053
GUCCAAGCUUUGAGUGGGAGCACCCCAUCUCAAAGUUA---CAAAUGCGCGAAGCGCAAUGCAAC-AAAACU-AAAAUUGGAUUCUAAGAAAACAUUAAA
((((((((((((((((((.....)))).))))))))).---....(((((...))))).......-......-.....)))))................. ( -28.00)
>DroPse_CAF1 49085 95 + 1
AUCCAAGCUUUGAGUUGAUC-CCUCAACCUCAAGGCUG---CAACUGCGCGAGGCGCAAUGUAAAGCAAACG-AAAAUUGGACCCAAACAAAAGAAAACU
.(((((((((((((((((..-..)))).))))))))((---((..(((((...))))).)))).........-....))))).................. ( -26.40)
>DroGri_CAF1 61007 92 + 1
AUCCAAGCUUUAGGAUAAUC--CUCAACCU-AAAGCUACACAAACUGCGCGAGGCGCAAUGUAAACAACACAAUCAAAUGGGCUCGA-----ACAUAAAA
.(((((((((((((......--.....)))-))))))..(((...(((((...))))).)))................)))).....-----........ ( -20.60)
>DroSec_CAF1 49377 95 + 1
GUCCAAGCUUUGAGUGGGUCCACCCCAUCUCAAAGUUA---CAAAUGCGCGAAGCGCAAUGCAAC-AACACU-GAAAUUGGAUUCUAAGAAAACAUAAAA
((((((((((((((((((.....)))).))))))))).---....(((((...))))).......-......-.....)))))................. ( -27.50)
>DroEre_CAF1 50214 95 + 1
GUCCAAGCUUUGAGUGGGUGCACCCCAGCUCAAAGUUA---UAAGUGCGCGAAGCGCAAUGCAAG-AAAACU-GAAAUUGGAUUCUAACAAAACAUAAAA
((((((((((((((((((.....)))).))))))))).---....(((((...))))).......-......-.....)))))................. ( -27.40)
>DroPer_CAF1 48130 95 + 1
AUCCAAGCUUUGAGUUGAUC-CCUCAACCUCAAGGCUG---CAACUGCGCGAGGCGCAAUGUAAAGCAAACG-AAAAUUGGACCCAAACAAAAGAAAACU
.(((((((((((((((((..-..)))).))))))))((---((..(((((...))))).)))).........-....))))).................. ( -26.40)
>consensus
AUCCAAGCUUUGAGUGGAUC_ACCCAACCUCAAAGCUA___CAACUGCGCGAAGCGCAAUGCAAA_AAAACU_AAAAUUGGACUCUAACAAAACAUAAAA
.(((((((((((((((((.....)))).)))))))))........(((((...)))))....................)))).................. (-24.97 = -23.72 +  -1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,567,141 – 25,567,236
Length 95
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 74.69
Mean single sequence MFE -26.62
Consensus MFE -19.42
Energy contribution -19.45
Covariance contribution 0.03
Combinations/Pair 1.14
Mean z-score -2.11
Structure conservation index 0.73
SVM decision value 2.06
SVM RNA-class probability 0.987035
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25567141 95 - 27905053
UUUAAUGUUUUCUUAGAAUCCAAUUUU-AGUUUU-GUUGCAUUGCGCUUCGCGCAUUUG---UAACUUUGAGAUGGGGUGCUCCCACUCAAAGCUUGGAC
..................(((((....-......-((((((.(((((...)))))..))---))))((((((.((((.....))))))))))..))))). ( -28.90)
>DroPse_CAF1 49085 95 - 1
AGUUUUCUUUUGUUUGGGUCCAAUUUU-CGUUUGCUUUACAUUGCGCCUCGCGCAGUUG---CAGCCUUGAGGUUGAGG-GAUCAACUCAAAGCUUGGAU
.................((((((....-....(((.....(((((((...))))))).)---))((.(((((.((((..-..))))))))).)))))))) ( -25.70)
>DroGri_CAF1 61007 92 - 1
UUUUAUGU-----UCGAGCCCAUUUGAUUGUGUUGUUUACAUUGCGCCUCGCGCAGUUUGUGUAGCUUU-AGGUUGAG--GAUUAUCCUAAAGCUUGGAU
......((-----((((((............((((..((.(((((((...))))))).))..))))(((-(((.(((.--..))).)))))))))))))) ( -23.60)
>DroSec_CAF1 49377 95 - 1
UUUUAUGUUUUCUUAGAAUCCAAUUUC-AGUGUU-GUUGCAUUGCGCUUCGCGCAUUUG---UAACUUUGAGAUGGGGUGGACCCACUCAAAGCUUGGAC
..................(((((....-......-((((((.(((((...)))))..))---))))((((((.((((.....))))))))))..))))). ( -30.10)
>DroEre_CAF1 50214 95 - 1
UUUUAUGUUUUGUUAGAAUCCAAUUUC-AGUUUU-CUUGCAUUGCGCUUCGCGCACUUA---UAACUUUGAGCUGGGGUGCACCCACUCAAAGCUUGGAC
..(((((...(((.((((..(......-.)..))-)).))).(((((...)))))..))---)))(((((((.((((.....)))))))))))....... ( -25.70)
>DroPer_CAF1 48130 95 - 1
AGUUUUCUUUUGUUUGGGUCCAAUUUU-CGUUUGCUUUACAUUGCGCCUCGCGCAGUUG---CAGCCUUGAGGUUGAGG-GAUCAACUCAAAGCUUGGAU
.................((((((....-....(((.....(((((((...))))))).)---))((.(((((.((((..-..))))))))).)))))))) ( -25.70)
>consensus
UUUUAUGUUUUGUUAGAAUCCAAUUUU_AGUUUU_UUUACAUUGCGCCUCGCGCAGUUG___UAACUUUGAGGUGGAGU_GACCAACUCAAAGCUUGGAC
..................(((((...................(((((...)))))..........(((((((.((((.....))))))))))).))))). (-19.42 = -19.45 +   0.03)

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 13:39:32 2006