Locus 7450

Sequence ID X_DroMel_CAF1
Location 18,604,814 – 18,605,002
Length 188
Max. P 0.968156
window12215 window12216 window12217 window12218

overview

Window 5

Location 18,604,814 – 18,604,927
Length 113
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 83.92
Mean single sequence MFE -21.68
Consensus MFE -13.24
Energy contribution -12.80
Covariance contribution -0.44
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.61
SVM decision value 0.03
SVM RNA-class probability 0.546636
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18604814 113 + 22224390
AAGAGUUCCUGCCCGAAUGUUGAGCUUCAACUCGUUAAAGUUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA--AAA
..(((((...((.(((...))).))...)))))(((((((((......)))))))))...(((((((..((((((.........))))))...(......)...))))))--).. ( -22.30)
>DroSec_CAF1 65852 113 + 1
AAGUUUUCCUGCCCGAAUGUCGAGCUUAAACUCGUUAAAGUUCAUUCAGACUUUAAUGCCUUCGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAA
(((((((.(((((....(((((((........((((((((((......))))))))))..)))))))...)))))....)))))))........................--... ( -24.70)
>DroSim_CAF1 64074 113 + 1
AAGUUUUCCUGCCCGAAUGUCGAGCUUCAACUCGUUAAAGUUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAA
(((((((.(((((....(((((((......)))(((((((((......)))))))))......))))...)))))....)))))))........................--... ( -23.90)
>DroYak_CAF1 57188 103 + 1
------------CUGAAAGUCCAGCUUCAACUUGUUAAAGUUCUUUUAGAACCCAAAGCCUUUGACAACUGCCAACUGAAAAACUUGGCAAACACAAUAAUAAAUGUCGAACAAA
------------(((......))).(((.(((((((((((..((((........)))).))))))))).((((((.(.....).))))))...............)).))).... ( -15.80)
>consensus
AAGUUUUCCUGCCCGAAUGUCGAGCUUCAACUCGUUAAAGUUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA__AAA
.....................(((......)))(((((((..((((........)))).)))))))...((((((.........))))))......................... (-13.24 = -12.80 +  -0.44)

alignment

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secondary structure

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Window 6

Location 18,604,854 – 18,604,967
Length 113
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 76.66
Mean single sequence MFE -19.72
Consensus MFE -10.02
Energy contribution -10.40
Covariance contribution 0.38
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.51
SVM decision value 1.62
SVM RNA-class probability 0.968156
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18604854 113 + 22224390
UUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGAUAAAGGCU
...................((((((....((((((.........))))))....((((.((.(((((...--...))))).))..))))...))))))((((.........)))) ( -19.70)
>DroSec_CAF1 65892 113 + 1
UUCAUUCAGACUUUAAUGCCUUCGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCU
.................(((((.(.....((((((.........))))))....((((.((.(((((...--...))))).))..))))..................).))))). ( -17.20)
>DroSim_CAF1 64114 113 + 1
UUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCU
.................(((((((.....((((((.........))))))....((((.((.(((((...--...))))).))..))))..................))))))). ( -21.30)
>DroEre_CAF1 52977 99 + 1
GUUUUCCAGACCUU-------------AAUGCCAACUGAAAGACUUGGCAAAC-CAAUCAUGAAUGCUGAACCAAACAUUAAUGCACUCAAAUCAAUGGGGCAAAGGUCA--GCU
........((((((-------------..((((...(((..((.((((....)-))))).(((.(((................))).)))..)))....)))))))))).--... ( -23.29)
>DroYak_CAF1 57216 109 + 1
UUCUUUUAGAACCCAAAGCCUUUGACAACUGCCAACUGAAAAACUUGGCAAACACAAUAAUAAAUGUCGAACAAAACAUCAA------CAAAUCAAUGAGGUAAAAACCAAGGCA
.................((((((((....((((((.(.....).))))))..............(((.((........)).)------))..)))....(((....)))))))). ( -17.10)
>consensus
UUCAUUCAGACUUUAAUGCCUUUGACAACUGGCAGCUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA__AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCU
.................(((((.......((((((.........))))))............(((((........))))).............................))))). (-10.02 = -10.40 +   0.38)

alignment

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secondary structure

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Window 7

Location 18,604,854 – 18,604,967
Length 113
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 76.66
Mean single sequence MFE -26.54
Consensus MFE -15.08
Energy contribution -15.78
Covariance contribution 0.70
Combinations/Pair 1.25
Mean z-score -2.00
Structure conservation index 0.57
SVM decision value 0.96
SVM RNA-class probability 0.890298
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18604854 113 - 22224390
AGCCUUUAUCUUUGGCUCUUUGAUUUGAAUGCAUUAAUGUUUU--UUGACAUUUAUUAUUCUGUUUGGCAAGUUUUUUAGCUGCCAGUUGUCAAAGGCAUUAAAGUCUGAAUGAA
((.(((((......((.(((((((..(((((.((.((((((..--..)))))).)))))))...((((((.(((....)))))))))..)))))))))..))))).))....... ( -26.40)
>DroSec_CAF1 65892 113 - 1
AGCCUUUGUCUUUGGCUCUUUGAUUUGAAUGCAUUAAUGUUUU--CUGACAUUUAUUAUUCUGUUUGGCAAGUUUUUUAGCUGCCAGUUGUCGAAGGCAUUAAAGUCUGAAUGAA
((.(((((((((((((..........(((((.((.((((((..--..)))))).)))))))...((((((.(((....)))))))))..))))))))))...))).))....... ( -27.70)
>DroSim_CAF1 64114 113 - 1
AGCCUUUGUCUUUGGCUCUUUGAUUUGAAUGCAUUAAUGUUUU--CUGACAUUUAUUAUUCUGUUUGGCAAGUUUUUUAGCUGCCAGUUGUCAAAGGCAUUAAAGUCUGAAUGAA
((.(((((((((((((..........(((((.((.((((((..--..)))))).)))))))...((((((.(((....)))))))))..))))))))))...))).))....... ( -28.00)
>DroEre_CAF1 52977 99 - 1
AGC--UGACCUUUGCCCCAUUGAUUUGAGUGCAUUAAUGUUUGGUUCAGCAUUCAUGAUUG-GUUUGCCAAGUCUUUCAGUUGGCAUU-------------AAGGUCUGGAAAAC
...--.((((((((((..(((((..(((((((................))))))).(((((-(....)).))))..))))).))))..-------------))))))........ ( -26.89)
>DroYak_CAF1 57216 109 - 1
UGCCUUGGUUUUUACCUCAUUGAUUUG------UUGAUGUUUUGUUCGACAUUUAUUAUUGUGUUUGCCAAGUUUUUCAGUUGGCAGUUGUCAAAGGCUUUGGGUUCUAAAAGAA
.((((.((((((((((.((.((((.((------((((........))))))...)))).)).).(((((((.(.....).)))))))..)).)))))))..)))).......... ( -23.70)
>consensus
AGCCUUUGUCUUUGGCUCUUUGAUUUGAAUGCAUUAAUGUUUU__UUGACAUUUAUUAUUCUGUUUGGCAAGUUUUUUAGCUGCCAGUUGUCAAAGGCAUUAAAGUCUGAAUGAA
.(((((((...(((((.....((((((........((((((......))))))...............))))))........)))))....)))))))................. (-15.08 = -15.78 +   0.70)

alignment

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secondary structure

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Window 8

Location 18,604,889 – 18,605,002
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.48
Mean single sequence MFE -19.49
Consensus MFE -4.34
Energy contribution -5.78
Covariance contribution 1.44
Combinations/Pair 1.20
Mean z-score -2.19
Structure conservation index 0.22
SVM decision value 1.61
SVM RNA-class probability 0.967669
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18604889 113 + 22224390
CUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGAUAAAGGCUUUCACCAAAAAAGUU--AUUUA---UAGUUUUUGCUCGGC
...........(((.....((((.((.(((((...--...))))).))..))))........((((.(((.(((((((((((.......))))))--.))))---)...))).))))))) ( -18.50)
>DroSec_CAF1 65927 115 + 1
CUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCUUUCACAAAAAUAUAUAUAGUUA---UAGUUUUUGCUCGGC
...........(((.....((((.((.(((((...--...))))).))..))))........((((.((((((.(..(((.................)))..---).))))))))))))) ( -19.03)
>DroSim_CAF1 64149 110 + 1
CUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAG--AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCUUUCACAAAAAA-----AAGUUA---UAGUUUUUGCUCGGC
...........(((.....((((.((.(((((...--...))))).))..))))........((((.((((((.(..(((((........)-----))))..---).))))))))))))) ( -21.70)
>DroEre_CAF1 52999 108 + 1
CUGAAAGACUUGGCAAAC-CAAUCAUGAAUGCUGAACCAAACAUUAAUGCACUCAAAUCAAUGGGGCAAAGGUCA--GCUCUCGAAAA---------AGUUAUUGUAGUUAGAGCCUUGA
((((...((((((....)-)))...(((..(((((.((.........(((.((((......)))))))..)))))--))..)))....---------.......))..))))........ ( -19.20)
>DroYak_CAF1 57251 103 + 1
CUGAAAAACUUGGCAAACACAAUAAUAAAUGUCGAACAAAACAUCAA------CAAAUCAAUGAGGUAAAAACCAAGGCAUUCGAAAA--------AAGUUA---UAGUUUUUGCCUUGA
........(..((((((.((.(((((.....(((((.......(((.------........)))(((....)))......)))))...--------..))))---).)).))))))..). ( -19.00)
>consensus
CUAAAAAACUUGCCAAACAGAAUAAUAAAUGUCAA__AAAACAUUAAUGCAUUCAAAUCAAAGAGCCAAAGACAAAGGCUUUCACAAAAA_______AGUUA___UAGUUUUUGCUCGGC
...(((((((.....(((.........(((((........))))).................(((((.........))))).................))).....)))))))....... ( -4.34 =  -5.78 +   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 12:39:13 2006