Locus 2570

Sequence ID 3L_DroMel_CAF1
Location 7,187,682 – 7,187,817
Length 135
Max. P 0.994100
window3983 window3984 window3985 window3986

overview

Window 3

Location 7,187,682 – 7,187,777
Length 95
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 84.08
Mean single sequence MFE -34.90
Consensus MFE -17.60
Energy contribution -19.00
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -3.14
Structure conservation index 0.50
SVM decision value 0.81
SVM RNA-class probability 0.857468
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7187682 95 + 23771897
AACAAUAAAACUUCCGCUUU-GGCGUUGAAGUUGUAGUUGACGUUGGCAAAUGCCACAACUGAGGGUUUUAAGCC-CCC-AGUGGGUGUGGCAAAGCC
..((((..(((((((((...-.)))..))))))...)))).....(((...(((((((((((.((((.....)))-).)-)))...)))))))..))) ( -36.00)
>DroPse_CAF1 54653 86 + 1
AACAAUAAAACUUCAGCUUUUGCCGUUGAUGUUGAAGUUGACGUUGGCAAAUGCCAG-----CGGC------GCCUCCCCAG-GGGCGUGGAAAAGCC
...............((((((.((((..((......))..))((((((....)))))-----).((------(((((....)-)))))))))))))). ( -33.00)
>DroSim_CAF1 51177 96 + 1
AACAAUAAAACUUCCGCUUU-GGCGUUGAAGUUGUAGUUGACGUUGGCAAAUGCCACAACUGAGGGUUUUUAGCCCCCC-AGUGGGCGUGGCAAAGCC
..((((..(((((((((...-.)))..))))))...)))).....(((...((((((.((((.((((.....))))..)-)))....))))))..))) ( -33.80)
>DroYak_CAF1 54832 95 + 1
AACAAUAAAACUUCCGCUUU-GCCGUUGAAGUUGUAGUUGACGUUGGCAAAUGCCACAACUGAGGGUUUUCCGAC-CCC-AGUGGGCGUGGCAAAGCC
...............(((((-(((((..(.(((......))).)..))..(((((...((((.(((((....)))-)))-))).))))))))))))). ( -38.70)
>DroPer_CAF1 63761 86 + 1
AACAAUAAAACUUCAGCUUUUGCCGUUGAUGUUGAAGUUGACGUUGGCAAAUGCCAG-----CGGC------GCCUCCCCAG-GGGCGUGGAAAAGCC
...............((((((.((((..((......))..))((((((....)))))-----).((------(((((....)-)))))))))))))). ( -33.00)
>consensus
AACAAUAAAACUUCCGCUUU_GCCGUUGAAGUUGUAGUUGACGUUGGCAAAUGCCACAACUGAGGGUUUU__GCC_CCC_AGUGGGCGUGGCAAAGCC
..((((..((((((.((.......)).))))))...)))).....(((...((((((......((........)).(((....))).))))))..))) (-17.60 = -19.00 +   1.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,187,682 – 7,187,777
Length 95
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 84.08
Mean single sequence MFE -31.70
Consensus MFE -18.42
Energy contribution -19.42
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 0.58
SVM decision value 0.93
SVM RNA-class probability 0.883784
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7187682 95 - 23771897
GGCUUUGCCACACCCACU-GGG-GGCUUAAAACCCUCAGUUGUGGCAUUUGCCAACGUCAACUACAACUUCAACGCC-AAAGCGGAAGUUUUAUUGUU
(((..(((((((...(((-(((-((.......)))))))))))))))...))).....(((.((.((((((..(((.-...))))))))).))))).. ( -37.10)
>DroPse_CAF1 54653 86 - 1
GGCUUUUCCACGCCC-CUGGGGAGGC------GCCG-----CUGGCAUUUGCCAACGUCAACUUCAACAUCAACGGCAAAAGCUGAAGUUUUAUUGUU
.((((..(((.....-.)))..))))------((((-----.((((....))))..((........)).....)))).(((((....)))))...... ( -24.60)
>DroSim_CAF1 51177 96 - 1
GGCUUUGCCACGCCCACU-GGGGGGCUAAAAACCCUCAGUUGUGGCAUUUGCCAACGUCAACUACAACUUCAACGCC-AAAGCGGAAGUUUUAUUGUU
(((..(((((((...(((-(((((........)))))))))))))))...))).....(((.((.((((((..(((.-...))))))))).))))).. ( -38.00)
>DroYak_CAF1 54832 95 - 1
GGCUUUGCCACGCCCACU-GGG-GUCGGAAAACCCUCAGUUGUGGCAUUUGCCAACGUCAACUACAACUUCAACGGC-AAAGCGGAAGUUUUAUUGUU
(((..(((((((...(((-(((-((......)))).)))))))))))...)))..................(((((.-(((((....))))).))))) ( -34.20)
>DroPer_CAF1 63761 86 - 1
GGCUUUUCCACGCCC-CUGGGGAGGC------GCCG-----CUGGCAUUUGCCAACGUCAACUUCAACAUCAACGGCAAAAGCUGAAGUUUUAUUGUU
.((((..(((.....-.)))..))))------((((-----.((((....))))..((........)).....)))).(((((....)))))...... ( -24.60)
>consensus
GGCUUUGCCACGCCCACU_GGG_GGC__AAAACCCUCAGUUGUGGCAUUUGCCAACGUCAACUACAACUUCAACGGC_AAAGCGGAAGUUUUAUUGUU
(((..((((((.(((....))).((........))......))))))...)))..................((((...(((((....)))))..)))) (-18.42 = -19.42 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,187,720 – 7,187,817
Length 97
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 66.91
Mean single sequence MFE -33.40
Consensus MFE -16.08
Energy contribution -16.83
Covariance contribution 0.75
Combinations/Pair 1.27
Mean z-score -2.41
Structure conservation index 0.48
SVM decision value 2.31
SVM RNA-class probability 0.992198
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7187720 97 + 23771897
GACGUUGGCAAAUGCCACAACUGAGGGUUUUAAGCC-CCC----------------AGUGGGUGUGGCAAAGCCCACGAAGUGCCAGCAGGAGGCCAAAUAGAAGCCAAGCAAA
...(((((((...(((...((((.((((.....)))-).)----------------))).)))((((......))))....)))))))....(((.........)))....... ( -34.90)
>DroPse_CAF1 54692 80 + 1
GACGUUGGCAAAUGCCAG-----CGGC------GCCUCCCC---------------AG-GGGCGUGGAAAAGCCC-CAAAGUGUCAAGA------AAAACUGAAAUUAUGAAGA
...((((((....)))))-----)(((------((......---------------.(-((((........))))-)...)))))....------................... ( -25.40)
>DroSim_CAF1 51215 98 + 1
GACGUUGGCAAAUGCCACAACUGAGGGUUUUUAGCCCCCC----------------AGUGGGCGUGGCAAAGCCCACGAAGUGCCGGCAGGAGACCAAAUAGAAGCCAAGCAAA
....(((((...((((...(((..((((.....))))...----------------.((((((........))))))..)))...))))(....).........)))))..... ( -34.20)
>DroYak_CAF1 54870 97 + 1
GACGUUGGCAAAUGCCACAACUGAGGGUUUUCCGAC-CCC----------------AGUGGGCGUGGCAAAGCCCACGAAGUGCCAGCAGGCGGCCAAAUAGAAGCCAAGCAAA
...(((((((...(((...((((.(((((....)))-)))----------------))).)))((((......))))....))))))).(((..(......)..)))....... ( -39.20)
>DroAna_CAF1 49317 103 + 1
GAUGUU-------GCCACAACUGCGACU----GGCCUCCUCGGGGGCCGGCGAGAGUGUGGGCGUGGUCCGGCCCCCGAAGUGCCAGCUGAAAGCCAAACAGAAGCCAAGCAAA
...(((-------((.......)))))(----(((((..(((((((((.((....))..((((...))))))))))))))).))))(((....((.........))..)))... ( -41.30)
>DroPer_CAF1 63800 80 + 1
GACGUUGGCAAAUGCCAG-----CGGC------GCCUCCCC---------------AG-GGGCGUGGAAAAGCCC-CAAAGUGUCAAGA------AAAACUGAAAUUAUGAAGA
...((((((....)))))-----)(((------((......---------------.(-((((........))))-)...)))))....------................... ( -25.40)
>consensus
GACGUUGGCAAAUGCCACAACUGAGGCU_____GCCUCCC________________AGUGGGCGUGGCAAAGCCCACGAAGUGCCAGCAGGAGGCCAAACAGAAGCCAAGCAAA
...(((((((....((........))...............................((((((........))))))....))))))).......................... (-16.08 = -16.83 +   0.75)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,187,720 – 7,187,817
Length 97
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 66.91
Mean single sequence MFE -35.88
Consensus MFE -12.20
Energy contribution -13.07
Covariance contribution 0.86
Combinations/Pair 1.08
Mean z-score -2.84
Structure conservation index 0.34
SVM decision value 2.45
SVM RNA-class probability 0.994100
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7187720 97 - 23771897
UUUGCUUGGCUUCUAUUUGGCCUCCUGCUGGCACUUCGUGGGCUUUGCCACACCCACU----------------GGG-GGCUUAAAACCCUCAGUUGUGGCAUUUGCCAACGUC
..((((.((((.......)))).......))))...(((.(((..(((((((...(((----------------(((-((.......)))))))))))))))...))).))).. ( -39.00)
>DroPse_CAF1 54692 80 - 1
UCUUCAUAAUUUCAGUUUU------UCUUGACACUUUG-GGGCUUUUCCACGCCC-CU---------------GGGGAGGC------GCCG-----CUGGCAUUUGCCAACGUC
...................------....(((.....(-(.((((..(((.....-.)---------------))..))))------.))(-----.((((....)))).)))) ( -24.40)
>DroSim_CAF1 51215 98 - 1
UUUGCUUGGCUUCUAUUUGGUCUCCUGCCGGCACUUCGUGGGCUUUGCCACGCCCACU----------------GGGGGGCUAAAAACCCUCAGUUGUGGCAUUUGCCAACGUC
..((((.(((................)))))))...(((.(((..(((((((...(((----------------(((((........)))))))))))))))...))).))).. ( -40.09)
>DroYak_CAF1 54870 97 - 1
UUUGCUUGGCUUCUAUUUGGCCGCCUGCUGGCACUUCGUGGGCUUUGCCACGCCCACU----------------GGG-GUCGGAAAACCCUCAGUUGUGGCAUUUGCCAACGUC
.......((((.......))))(((....)))....(((.(((..(((((((...(((----------------(((-((......)))).)))))))))))...))).))).. ( -39.60)
>DroAna_CAF1 49317 103 - 1
UUUGCUUGGCUUCUGUUUGGCUUUCAGCUGGCACUUCGGGGGCCGGACCACGCCCACACUCUCGCCGGCCCCCGAGGAGGCC----AGUCGCAGUUGUGGC-------AACAUC
.((((..((((.......))))....((((((.(((((((((((((.....(......).....)))))))))))))..)))----))).))))..(((..-------..))). ( -47.80)
>DroPer_CAF1 63800 80 - 1
UCUUCAUAAUUUCAGUUUU------UCUUGACACUUUG-GGGCUUUUCCACGCCC-CU---------------GGGGAGGC------GCCG-----CUGGCAUUUGCCAACGUC
...................------....(((.....(-(.((((..(((.....-.)---------------))..))))------.))(-----.((((....)))).)))) ( -24.40)
>consensus
UUUGCUUGGCUUCUAUUUGGCCUCCUGCUGGCACUUCGUGGGCUUUGCCACGCCCACU________________GGGAGGC_____ACCCGCAGUUGUGGCAUUUGCCAACGUC
.............................(((.....((((((........))))))........................................((((....))))..))) (-12.20 = -13.07 +   0.86)

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 10:35:53 2006