Locus 714

Sequence ID 3L_DroMel_CAF1
Location 2,166,673 – 2,166,805
Length 132
Max. P 0.985815
window1092 window1093 window1094 window1095

overview

Window 2

Location 2,166,673 – 2,166,776
Length 103
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 74.13
Mean single sequence MFE -27.14
Consensus MFE -16.34
Energy contribution -16.03
Covariance contribution -0.30
Combinations/Pair 1.21
Mean z-score -2.24
Structure conservation index 0.60
SVM decision value 2.02
SVM RNA-class probability 0.985815
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2166673 103 + 23771897
AUGGGUAUUGGGAUAAUGCGUUUUCCUUGACUUGCCGCCGAAUGCUUUAAAGUGCAUCAAUUUUAAUGCAAA--U---------GCA-GCAAGCAGCAUUAACUCUUGUUGCACU
...((((..((((..........)))).....))))......(((.(((((((......))))))).)))..--(---------(((-(((((.((......))))))))))).. ( -26.70)
>DroPse_CAF1 256756 100 + 1
CAGGGUAUUCG-GCAAUG-----------CCUUUCGCCCGAAUGCUUUAAAGUGCAUCAAUUUUAAUGCAAA--UAUGCAGCAAGCA-GCAAGCAGCAUUAACUUUUGCUGCGCU
.((((((((((-(....(-----------(.....)))))))))))))..((((((.(((..(((((((...--..(((.....)))-.......)))))))...))).)))))) ( -30.40)
>DroSec_CAF1 218671 96 + 1
AUAGGUAU-------AUGCGUUUUCCUUGACUUGCAGCCGAAUGCUUUAAAGUGCAUCAAUUUUAAUGCAAA--U---------GCA-GCAAGCAGCAUUAACUCUUGCUGCACU
...(((..-------.((((((......)))..))))))...(((.(((((((......))))))).)))..--(---------(((-(((((.((......))))))))))).. ( -27.00)
>DroWil_CAF1 269875 86 + 1
CAGGGUAUUGGGC--------------------CCAUCCAAAUGUUUUAAAGUGCAUCAAUUUUAAUGCAAA--UAU-------GCAGGCAAGCAGCAUUAACUUUUGCUGCGCU
..((((.....))--------------------))...............((((((.(((..(((((((...--..(-------((......))))))))))...))).)))))) ( -23.00)
>DroAna_CAF1 214375 103 + 1
CAGGGUAUC-GGAUAAUGCUUUCGCUUUGACUCGCAUCCGAUUGCU-UAAAGUGCAUCAAUUUUAAUGCAAAUAU---------GCA-GCAAGCAGCAUUAACUUUGGCUGUGCU
((.(((...-((.(((((((...((((.(.((.((((....(((((-((((((......))))))).))))..))---------)))-))))))))))))).))...))).)).. ( -27.00)
>DroPer_CAF1 236406 100 + 1
CAGGGUAUUCG-GCAAUG-----------CCUUUCGCCCGAAUGCUUUAAAGUGCAUCAAUUUUAAUGCAAA--UAUUCAGCAAGCA-GCAAGCAGCAUUAACUUUUGCUGCGCU
..((((....(-((...)-----------))....))))...((((......(((((........)))))..--.....)))).(((-(((((.((......))))))))))... ( -28.72)
>consensus
CAGGGUAUU_G_A_AAUG___________ACUUGCACCCGAAUGCUUUAAAGUGCAUCAAUUUUAAUGCAAA__U_________GCA_GCAAGCAGCAUUAACUUUUGCUGCGCU
...(((....................................(((.(((((((......))))))).)))......................((((((........))))))))) (-16.34 = -16.03 +  -0.30)

alignment

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secondary structure

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Window 3

Location 2,166,673 – 2,166,776
Length 103
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.13
Mean single sequence MFE -26.59
Consensus MFE -13.25
Energy contribution -13.75
Covariance contribution 0.50
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.50
SVM decision value 1.20
SVM RNA-class probability 0.930161
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2166673 103 - 23771897
AGUGCAACAAGAGUUAAUGCUGCUUGC-UGC---------A--UUUGCAUUAAAAUUGAUGCACUUUAAAGCAUUCGGCGGCAAGUCAAGGAAAACGCAUUAUCCCAAUACCCAU
((((((((....)))..((((((((((-(..---------.--..(((((((....)))))))......))))...))))))).............))))).............. ( -25.40)
>DroPse_CAF1 256756 100 - 1
AGCGCAGCAAAAGUUAAUGCUGCUUGC-UGCUUGCUGCAUA--UUUGCAUUAAAAUUGAUGCACUUUAAAGCAUUCGGGCGAAAGG-----------CAUUGC-CGAAUACCCUG
...(((((((.(((....)))..))))-))).((((.....--..(((((((....)))))))......))))...(((.....((-----------(...))-).....))).. ( -30.92)
>DroSec_CAF1 218671 96 - 1
AGUGCAGCAAGAGUUAAUGCUGCUUGC-UGC---------A--UUUGCAUUAAAAUUGAUGCACUUUAAAGCAUUCGGCUGCAAGUCAAGGAAAACGCAU-------AUACCUAU
((((((((((((((....))).)))))-)))---------)--))(((((((....))))))).......((....(((.....)))..(.....)))..-------........ ( -27.60)
>DroWil_CAF1 269875 86 - 1
AGCGCAGCAAAAGUUAAUGCUGCUUGCCUGC-------AUA--UUUGCAUUAAAAUUGAUGCACUUUAAAACAUUUGGAUGG--------------------GCCCAAUACCCUG
...((((((........))))))..((((..-------...--..(((((((....))))))).(((((.....))))).))--------------------))........... ( -19.20)
>DroAna_CAF1 214375 103 - 1
AGCACAGCCAAAGUUAAUGCUGCUUGC-UGC---------AUAUUUGCAUUAAAAUUGAUGCACUUUA-AGCAAUCGGAUGCGAGUCAAAGCGAAAGCAUUAUCC-GAUACCCUG
((((.(((...(((....)))))))))-)((---------.((..(((((((....)))))))...))-.)).((((((((.(...)...((....))..)))))-)))...... ( -25.50)
>DroPer_CAF1 236406 100 - 1
AGCGCAGCAAAAGUUAAUGCUGCUUGC-UGCUUGCUGAAUA--UUUGCAUUAAAAUUGAUGCACUUUAAAGCAUUCGGGCGAAAGG-----------CAUUGC-CGAAUACCCUG
...(((((((.(((....)))..))))-))).((((.....--..(((((((....)))))))......))))...(((.....((-----------(...))-).....))).. ( -30.92)
>consensus
AGCGCAGCAAAAGUUAAUGCUGCUUGC_UGC_________A__UUUGCAUUAAAAUUGAUGCACUUUAAAGCAUUCGGAUGCAAGU___________CAUU_C_C_AAUACCCUG
.((((((((........))))))......................(((((((....))))))).......))........................................... (-13.25 = -13.75 +   0.50)

alignment

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secondary structure

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Window 4

Location 2,166,713 – 2,166,805
Length 92
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.26
Mean single sequence MFE -25.10
Consensus MFE -10.88
Energy contribution -10.93
Covariance contribution 0.06
Combinations/Pair 1.33
Mean z-score -3.02
Structure conservation index 0.43
SVM decision value 0.38
SVM RNA-class probability 0.714946
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2166713 92 + 23771897
AAUGCUUUAAAGUGCAUCAAUUU--UAAUGCAAA--U---------GCA-GCAAGCAGCAUUAACUCUUGUUGCACU-----CUUAAAAAUUUACAUAAUUGCUGAAAGUC
..(((.(((((((......))))--))).)))..--.---------.((-((((((((((........))))))...-----..(((....))).....))))))...... ( -20.10)
>DroVir_CAF1 240414 101 + 1
AAUGCUUUAAAGUGCAUCAAUUUAAUAAUGCAAA--CAU-------GCA-GCAAGUUGCAUUAACUUUUGCCGCGCAGGCGGCAUUAAAAUUUGCAUAAUUGCUGCGACUC
.((((........)))).................--..(-------(((-((((..((((........((((((....))))))........))))...)))))))).... ( -32.19)
>DroWil_CAF1 269895 95 + 1
AAUGUUUUAAAGUGCAUCAAUUU--UAAUGCAAA--UAU-------GCAGGCAAGCAGCAUUAACUUUUGCUGCGCU-----UUUACAAAUUUACAUAAUUGCUAAGAGUC
..(((...((((((((.(((..(--((((((...--..(-------((......))))))))))...))).))))))-----)).)))....................... ( -21.20)
>DroMoj_CAF1 220288 101 + 1
AAUGCUUUAAAGUGCAUUAAUUUAAUAAUGCAAA--CAU-------GCA-GCAAGUUGCAUUAACUCUCGCCGCGCAGGCGGCAUUAAAAUUUGCAUAAUUGCCGCGAGUC
...((((.....(((((((......)))))))..--...-------((.-((((..((((.........(((((....))))).........))))...)))).)))))). ( -29.47)
>DroAna_CAF1 214414 93 + 1
AUUGCU-UAAAGUGCAUCAAUUU--UAAUGCAAAUAU---------GCA-GCAAGCAGCAUUAACUUUGGCUGUGCU-----CUUAAAAAUUUGCAUAAUUGUUGAAAGUC
..(((.-......)))(((((..--(.((((((((..---------..(-((..(((((..........))))))))-----.......)))))))).)..)))))..... ( -20.10)
>DroPer_CAF1 236434 101 + 1
AAUGCUUUAAAGUGCAUCAAUUU--UAAUGCAAA--UAUUCAGCAAGCA-GCAAGCAGCAUUAACUUUUGCUGCGCU-----CUUAAAAAUUUACAUAAUUGCUGAGAGUC
..((((......(((((......--..)))))..--.....)))).(((-(((((.((......))))))))))(((-----((((..((((.....))))..))))))). ( -27.52)
>consensus
AAUGCUUUAAAGUGCAUCAAUUU__UAAUGCAAA__UAU_______GCA_GCAAGCAGCAUUAACUUUUGCUGCGCU_____CUUAAAAAUUUACAUAAUUGCUGAGAGUC
.((((........))))............((((.............(....)..((((((........)))))).........................))))........ (-10.88 = -10.93 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,166,713 – 2,166,805
Length 92
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -25.77
Consensus MFE -12.24
Energy contribution -10.80
Covariance contribution -1.44
Combinations/Pair 1.44
Mean z-score -2.92
Structure conservation index 0.47
SVM decision value 0.54
SVM RNA-class probability 0.774309
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2166713 92 - 23771897
GACUUUCAGCAAUUAUGUAAAUUUUUAAG-----AGUGCAACAAGAGUUAAUGCUGCUUGC-UGC---------A--UUUGCAUUA--AAAUUGAUGCACUUUAAAGCAUU
........((((((.....))))....((-----((((((.(((...((((((((((....-.))---------)--...))))))--)..))).))))))))...))... ( -22.90)
>DroVir_CAF1 240414 101 - 1
GAGUCGCAGCAAUUAUGCAAAUUUUAAUGCCGCCUGCGCGGCAAAAGUUAAUGCAACUUGC-UGC-------AUG--UUUGCAUUAUUAAAUUGAUGCACUUUAAAGCAUU
.....(((((((...((((((((((..((((((....))))))))))))..))))..))))-)))-------(((--(((((((((......)))))))......))))). ( -34.40)
>DroWil_CAF1 269895 95 - 1
GACUCUUAGCAAUUAUGUAAAUUUGUAAA-----AGCGCAGCAAAAGUUAAUGCUGCUUGCCUGC-------AUA--UUUGCAUUA--AAAUUGAUGCACUUUAAAACAUU
.........(((((((((((((.((((..-----.((((((((........))))))..)).)))-------).)--)))))))..--.)))))................. ( -20.80)
>DroMoj_CAF1 220288 101 - 1
GACUCGCGGCAAUUAUGCAAAUUUUAAUGCCGCCUGCGCGGCGAGAGUUAAUGCAACUUGC-UGC-------AUG--UUUGCAUUAUUAAAUUAAUGCACUUUAAAGCAUU
.....(((((((...((((((((((...(((((....))))).))))))..))))..))))-)))-------(((--(((((((((......)))))))......))))). ( -33.10)
>DroAna_CAF1 214414 93 - 1
GACUUUCAACAAUUAUGCAAAUUUUUAAG-----AGCACAGCCAAAGUUAAUGCUGCUUGC-UGC---------AUAUUUGCAUUA--AAAUUGAUGCACUUUA-AGCAAU
.....((((.....((((((((.......-----((((.(((...(((....)))))))))-)..---------..))))))))..--...))))(((......-.))).. ( -17.30)
>DroPer_CAF1 236434 101 - 1
GACUCUCAGCAAUUAUGUAAAUUUUUAAG-----AGCGCAGCAAAAGUUAAUGCUGCUUGC-UGCUUGCUGAAUA--UUUGCAUUA--AAAUUGAUGCACUUUAAAGCAUU
(.((((.((.((((.....)))).)).))-----)))(((((((.(((....)))..))))-))).((((.....--..(((((((--....)))))))......)))).. ( -26.12)
>consensus
GACUCUCAGCAAUUAUGCAAAUUUUUAAG_____AGCGCAGCAAAAGUUAAUGCUGCUUGC_UGC_______AUA__UUUGCAUUA__AAAUUGAUGCACUUUAAAGCAUU
..............((((................((((.(((....)))..))))........................(((((((......))))))).......)))). (-12.24 = -10.80 +  -1.44)

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 09:49:16 2006