Locus 5805

Sequence ID 2L_DroMel_CAF1
Location 16,460,544 – 16,460,666
Length 122
Max. P 0.886727
window9208 window9209 window9210

overview

Window 8

Location 16,460,544 – 16,460,644
Length 100
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 78.72
Mean single sequence MFE -36.65
Consensus MFE -20.01
Energy contribution -21.78
Covariance contribution 1.76
Combinations/Pair 1.11
Mean z-score -1.77
Structure conservation index 0.55
SVM decision value 0.08
SVM RNA-class probability 0.574314
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16460544 100 + 22407834
UUCGGCCGUC-UGGUCUAGGGACUAACUGCCCUAUAGAGGGGGCCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGGCUGCCAGGCAGUU-----GG--GGGCCGCUG
..(((((.((-.((((....))))((((.((((....)))).(((....((((((((.((((.(....).)))).)))))))))))))))-----))--.)))))... ( -40.80)
>DroSec_CAF1 85298 100 + 1
UUCGGCCGUC-UGGUCUAGGGACUAACUGCCCUAAAGAGGGGGCCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGGCUGCCAGGCAGUU-----GG--GGGCCGCUG
..(((((.((-.((((....))))((((.((((....)))).(((....((((((((.((((.(....).)))).)))))))))))))))-----))--.)))))... ( -40.80)
>DroEre_CAF1 82260 99 + 1
UUUGGCCGUC-UGGUCUAGGGACUAACUGCCCUAUGGAGGGGGCCAAAUUGGCGGCUUACUUGUGUGUGGAAAUUGCCUGCCAGGCAGUU-----GG---GGCCGCUG
(((((((((.-(((((....)))))))..((((....)))))))))))..((((((((((......))...(((((((.....)))))))-----.)---))))))). ( -42.10)
>DroYak_CAF1 87312 99 + 1
UUCGGCCGUC-UGGUCUAGGGAGUAUCUGCCCUAUGGAGGGGGCCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGCCUGCCAGGCAGUU-----GG---GGCCGCUG
...((((.((-(..(((((((........))))).))))).)))).....((((((((..((((.((.((......))...)).))))..-----.)---))))))). ( -38.90)
>DroAna_CAF1 78894 92 + 1
UUUGGCCUUUUUGGACUAUGG-------GCCU---AGUG-GGGGCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGCCUGCCAGACUGUA-----GCCUUUGCCGUUG
...(((......((.((((((-------((((---....-.))))...((((((((..((((.(....).)))).))).))))).)))))-----)))...))).... ( -29.10)
>DroPer_CAF1 58487 85 + 1
UCACGUUGUC-UGGUCUAGU-------------------GGGGGCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGCCUGCCAAGCUGUUUUUUUGC---UGCCGCUG
..........-.....((((-------------------((.((((((..(((((((....((.(((.((......))))))))))))))..)))))---).)))))) ( -28.20)
>consensus
UUCGGCCGUC_UGGUCUAGGGACUAACUGCCCUAUAGAGGGGGCCAAAUUGGCGGCUUAUUUGUGUGUGGAAAUUGCCUGCCAGGCAGUU_____GG___GGCCGCUG
..(((((....((((((((((........)))).......))))))..(((((((...((((.(....).))))...)))))))................)))))... (-20.01 = -21.78 +   1.76)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,460,544 – 16,460,644
Length 100
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 78.72
Mean single sequence MFE -26.76
Consensus MFE -14.95
Energy contribution -17.07
Covariance contribution 2.13
Combinations/Pair 1.16
Mean z-score -2.23
Structure conservation index 0.56
SVM decision value 0.94
SVM RNA-class probability 0.886727
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16460544 100 - 22407834
CAGCGGCCC--CC-----AACUGCCUGGCAGCCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUAUAGGGCAGUUAGUCCCUAGACCA-GACGGCCGAA
...(((((.--..-----(((((((((((.......................)))(((.....)))..........)))))))).(((.........-)))))))).. ( -30.30)
>DroSec_CAF1 85298 100 - 1
CAGCGGCCC--CC-----AACUGCCUGGCAGCCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUUUAGGGCAGUUAGUCCCUAGACCA-GACGGCCGAA
...(((((.--..-----(((((((((((.......................)))(((.....)))..........)))))))).(((.........-)))))))).. ( -30.30)
>DroEre_CAF1 82260 99 - 1
CAGCGGCC---CC-----AACUGCCUGGCAGGCAAUUUCCACACACAAGUAAGCCGCCAAUUUGGCCCCCUCCAUAGGGCAGUUAGUCCCUAGACCA-GACGGCCAAA
....((((---..-----(((((((((((.(((...................))))))....(((......)))..)))))))).(((.........-)))))))... ( -30.91)
>DroYak_CAF1 87312 99 - 1
CAGCGGCC---CC-----AACUGCCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCCAUAGGGCAGAUACUCCCUAGACCA-GACGGCCGAA
..(((((.---..-----...((((.....))))((((........))))..)))))...(((((((..((...(((((.((...)))))))....)-)..))))))) ( -28.70)
>DroAna_CAF1 78894 92 - 1
CAACGGCAAAGGC-----UACAGUCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGCCCC-CACU---AGGC-------CCAUAGUCCAAAAAGGCCAAA
....(((((((((-----....)))((((.(((...................))))))).))))))..-....---.(((-------(.............))))... ( -24.13)
>DroPer_CAF1 58487 85 - 1
CAGCGGCA---GCAAAAAAACAGCUUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGCCCCC-------------------ACUAGACCA-GACAACGUGA
.((.((..---(((((........(((((.(((...................)))))))))))))..))-------------------.))......-.......... ( -16.21)
>consensus
CAGCGGCC___CC_____AACUGCCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUAUAGGGCAGUUAGUCCCUAGACCA_GACGGCCGAA
..(((((.............((((...))))...((((........))))..)))))...(((((((.......(((((........))))).........))))))) (-14.95 = -17.07 +   2.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,460,573 – 16,460,666
Length 93
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 80.81
Mean single sequence MFE -24.35
Consensus MFE -12.92
Energy contribution -13.40
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.53
SVM decision value 0.18
SVM RNA-class probability 0.621023
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16460573 93 - 22407834
CC--UUUUACCC------UGGGCA----CAAAAACAGCGGCCC--CCAACUGCCUGGCAGCCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUAUAGG
((--(.......------.((((.----((((......(((..--......)))((((.((..((((........))))..)).)))).)))))))).......))) ( -22.46)
>DroSec_CAF1 85327 92 - 1
CC--UUUUACCC------UGGGCA----CAA-AACAGCGGCCC--CCAACUGCCUGGCAGCCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUUUAGG
((--(.......------.((((.----(((-(.....(((..--......)))((((.((..((((........))))..)).)))).)))))))).......))) ( -22.46)
>DroEre_CAF1 82289 94 - 1
CCAGUUUACCCC------UGGGCA----CAAGAACAGCGGCC---CCAACUGCCUGGCAGGCAAUUUCCACACACAAGUAAGCCGCCAAUUUGGCCCCCUCCAUAGG
............------.((((.----((((....(((((.---.....((((.....))))......((......))..)))))...))))))))(((....))) ( -23.60)
>DroYak_CAF1 87341 92 - 1
CC--UUAUACCC------UGGCCA----GAAGUACAGCGGCC---CCAACUGCCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCCAUAGG
((--(.......------.(((((----((......((((..---....)))).((((.(((...................))))))).)))))))........))) ( -24.80)
>DroAna_CAF1 78917 101 - 1
CC--UUCCACCUUUCAACGGGGCAGCCGCAGAAGCAACGGCAAAGGCUACAGUCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGCCCC-CACU---AG
..--..............((((((((((.........))))..((((....))))(((.(((...................))))))....))))))-....---.. ( -28.41)
>consensus
CC__UUUUACCC______UGGGCA____CAAAAACAGCGGCC___CCAACUGCCUGGCAGGCAAUUUCCACACACAAAUAAGCCGCCAAUUUGGCCCCCUCUAUAGG
...................((((...............(((..........)))((((.(((.((((........))))..))))))).....)))).......... (-12.92 = -13.40 +   0.48)

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 11:53:24 2006