Locus 3075

Sequence ID 3L_DroMel_CAF1
Location 8,900,015 – 8,900,161
Length 146
Max. P 0.922067
window4796 window4797 window4798

overview

Window 6

Location 8,900,015 – 8,900,123
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.17
Mean single sequence MFE -32.47
Consensus MFE -21.84
Energy contribution -21.70
Covariance contribution -0.14
Combinations/Pair 1.15
Mean z-score -2.75
Structure conservation index 0.67
SVM decision value 1.15
SVM RNA-class probability 0.922067
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8900015 108 + 23771897
UGCAGUUGAAGGUAGCUCCGUGGAG--GAAAACAGCCCCAAGAUUUCGAAAACAACGAAAAUGGUCUUCGACUGCGGAGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUU
.(((((((((((.....((((((.(--(.......))))....(((((.......)))))))))))))))))))).......((((((((((((....)))))))))))) ( -37.10)
>DroVir_CAF1 190391 100 + 1
UGCAGCCCGAG----UUU----GAA--AAAAACAGCCGCAAAAUUUCGAAAACAUCGAAAAUGGUCUUUGACUGUGGUGUCUGGUGUGCAAAGUAUUUGCUUUGCAUACU
..(((.....(----(((----...--..)))).(((((....((((((.....))))))..((((...)))))))))..)))(((((((((((....))))))))))). ( -31.00)
>DroPse_CAF1 193011 104 + 1
UGCAGUCGA---GUGCUCGAGUGAG--GA-AACAGCCGCAAGAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGUGGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUU
.((((((((---(.(((((.((..(--..-..).)))).....(((((.......)))))..))).))))))))).......((((((((((((....)))))))))))) ( -33.50)
>DroGri_CAF1 162933 99 + 1
UCCAGCGCAAG----UUC-------UUCAAAACAGCCGCAAAAUUUCGAAAACAUCGAAAAUGGUCUUUGAUUGUGGUGUUUGGUGUGCAAAGUAUUUGCUUUGCAUACU
...(((....)----)).-------..((((...((((((...((((((.....))))))...(((...))))))))).))))(((((((((((....))))))))))). ( -30.80)
>DroMoj_CAF1 190670 102 + 1
UGCAGCUCGAG----UUU----GUAUUAAAAACAGCCCCAAAAUUUCGAAAACAUCGAAAAUGGUCUUCGAUUGUGGUGUUUGGUGUGCAAAGUAUUUGCUUUGCAUACU
.((((.(((((----(((----.......))))....(((...((((((.....)))))).)))...)))))))).......((((((((((((....)))))))))))) ( -28.90)
>DroPer_CAF1 185881 104 + 1
UGCAGUCGA---GUGCUCGAGUGAG--GA-AACAGCCGCAAGAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGUGGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUU
.((((((((---(.(((((.((..(--..-..).)))).....(((((.......)))))..))).))))))))).......((((((((((((....)))))))))))) ( -33.50)
>consensus
UGCAGCCCAAG____CUC____GAG__GAAAACAGCCGCAAAAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGGUGUCUGGUGUGCAAAGUAUUUGCUUUGCAUACU
................................(((((((....(((((.......)))))..((((...))))))))...)))(((((((((((....))))))))))). (-21.84 = -21.70 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,900,015 – 8,900,123
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -24.97
Consensus MFE -16.65
Energy contribution -16.48
Covariance contribution -0.17
Combinations/Pair 1.09
Mean z-score -2.07
Structure conservation index 0.67
SVM decision value 0.66
SVM RNA-class probability 0.813325
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8900015 108 - 23771897
AAUAUGCAAAGCAAAUACUUUGCACACCAGACUCCGCAGUCGAAGACCAUUUUCGUUGUUUUCGAAAUCUUGGGGCUGUUUUC--CUCCACGGAGCUACCUUCAACUGCA
....(((((((......)))))))...........(((((.((((.(((.(((((.......)))))...)))(((.....((--(.....))))))..)))).))))). ( -30.20)
>DroVir_CAF1 190391 100 - 1
AGUAUGCAAAGCAAAUACUUUGCACACCAGACACCACAGUCAAAGACCAUUUUCGAUGUUUUCGAAAUUUUGCGGCUGUUUUU--UUC----AAA----CUCGGGCUGCA
.((.(((((((......))))))).))..(((......))).........((((((.....))))))...(((((((((((..--...----)))----)...))))))) ( -25.10)
>DroPse_CAF1 193011 104 - 1
AAUAUGCAAAGCAAAUACUUUGCACACCAGACCACGCAGUCAAAGACCAUUUUCGUUGUUUUCGAAAUCUUGCGGCUGUU-UC--CUCACUCGAGCAC---UCGACUGCA
....(((((((......)))))))...........((((((.((((....(((((.......)))))))))..(..((((-(.--.......))))).---.))))))). ( -25.50)
>DroGri_CAF1 162933 99 - 1
AGUAUGCAAAGCAAAUACUUUGCACACCAAACACCACAAUCAAAGACCAUUUUCGAUGUUUUCGAAAUUUUGCGGCUGUUUUGAA-------GAA----CUUGCGCUGGA
.((.(((((((......))))))).))...................(((.((((((.....))))))....(((...((((....-------)))----)...)))))). ( -21.20)
>DroMoj_CAF1 190670 102 - 1
AGUAUGCAAAGCAAAUACUUUGCACACCAAACACCACAAUCGAAGACCAUUUUCGAUGUUUUCGAAAUUUUGGGGCUGUUUUUAAUAC----AAA----CUCGAGCUGCA
.((.(((((((......))))))).))............((((((((.(((...)))))))))))...((((((..(((.......))----)..----))))))..... ( -22.30)
>DroPer_CAF1 185881 104 - 1
AAUAUGCAAAGCAAAUACUUUGCACACCAGACCACGCAGUCAAAGACCAUUUUCGUUGUUUUCGAAAUCUUGCGGCUGUU-UC--CUCACUCGAGCAC---UCGACUGCA
....(((((((......)))))))...........((((((.((((....(((((.......)))))))))..(..((((-(.--.......))))).---.))))))). ( -25.50)
>consensus
AAUAUGCAAAGCAAAUACUUUGCACACCAGACACCACAGUCAAAGACCAUUUUCGAUGUUUUCGAAAUCUUGCGGCUGUUUUC__CUC____GAA____CUUCGACUGCA
....(((((((......)))))))...........((((((.((((....(((((.......)))))))))..))))))............................... (-16.65 = -16.48 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,900,044 – 8,900,161
Length 117
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 84.32
Mean single sequence MFE -29.70
Consensus MFE -21.88
Energy contribution -21.93
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -2.31
Structure conservation index 0.74
SVM decision value 0.31
SVM RNA-class probability 0.681650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8900044 117 + 23771897
ACAGCCCCAAGAUUUCGAAAACAACGAAAAUGGUCUUCGACUGCGGAGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUUCAAUUUUAUAUUUUUCGUAAGUACAGAUGA-AGUAAU-GU
.......((..((((((...((.(((((((.((.(((((....))))).))((((((((((((....))))))))))))...........)))))))..)).....)))-)))..)-). ( -26.90)
>DroVir_CAF1 190412 118 + 1
ACAGCCGCAAAAUUUCGAAAACAUCGAAAAUGGUCUUUGACUGUGGUGUCUGGUGUGCAAAGUAUUUGCUUUGCAUACUGAAUUUCAUAUUUUUUGUGAGUAUAA-AUAAAGUACAAUU
...(((((....((((((.....))))))..((((...))))))))).((.((((((((((((....))))))))))))))...(((((.....)))))((((..-.....)))).... ( -33.40)
>DroPse_CAF1 193036 110 + 1
ACAGCCGCAAGAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGUGGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUUCAAUUUCAUAUUUUUCGUAAGUAUUGCCAA--------U-
......((((.((((((((((....((((.(((.....((((....))))..(((((((((((....)))))))))))))).))))....)))))).)))).))))...--------.- ( -29.30)
>DroGri_CAF1 162953 119 + 1
ACAGCCGCAAAAUUUCGAAAACAUCGAAAAUGGUCUUUGAUUGUGGUGUUUGGUGUGCAAAGUAUUUGCUUUGCAUACUAAAUUUCAUAUUCUUUGUAAGUAUACACAAUAUAACAAUU
......(((((.((((((.....)))))).........((.(((((.((((((((((((((((....)))))))))))))))).))))).)))))))...................... ( -33.50)
>DroAna_CAF1 157752 117 + 1
ACAGCCCCAAAAUUUCGAAAACAACGAAAAUGGUCUUCGACUGCGGAGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUUCAAUUUUAUAUUUUUUGUAAGUAUCUCGAG-CGUUAA-GU
.............(((((..((.(((((((.((.(((((....))))).))((((((((((((....))))))))))))...........)))))))..))...)))))-......-.. ( -25.80)
>DroPer_CAF1 185906 111 + 1
ACAGCCGCAAGAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGUGGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUUCAAUUUCAUAUUUUUCGUAAGUAUUGCCAA--------UU
......((((.((((((((((....((((.(((.....((((....))))..(((((((((((....)))))))))))))).))))....)))))).)))).))))...--------.. ( -29.30)
>consensus
ACAGCCGCAAAAUUUCGAAAACAACGAAAAUGGUCUUUGACUGCGGAGUCUGGUGUGCAAAGUAUUUGCUUUGCAUAUUCAAUUUCAUAUUUUUCGUAAGUAUAGCCAA_AGUA_A_UU
.(((((((....(((((.......)))))..((((...))))))))...)))(((((((((((....)))))))))))......................................... (-21.88 = -21.93 +   0.06)

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 10:48:56 2006