Locus 3589

Sequence ID X_DroMel_CAF1
Location 9,619,293 – 9,619,437
Length 144
Max. P 0.884973
window5876 window5877 window5878 window5879

overview

Window 6

Location 9,619,293 – 9,619,399
Length 106
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.11
Mean single sequence MFE -30.12
Consensus MFE -21.06
Energy contribution -21.32
Covariance contribution 0.25
Combinations/Pair 1.24
Mean z-score -1.92
Structure conservation index 0.70
SVM decision value 0.43
SVM RNA-class probability 0.731554
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9619293 106 + 22224390
GCAUAGGCCGCUUAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCAAUCGCCCCCUGCCUG------UGCCCC-UUUCCAAACCCACUUUUGGCCAAUUCGUUGGCCAU
((((((((.((...((((.......))))..((((((...(....))))))).)).....)))))------)))...-................(((((((....))))))). ( -34.80)
>DroSec_CAF1 79726 105 + 1
GCACAGGCCGCGAAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCACCCGCCCCCUUCCCA------UGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAU
.....(((((((((....(....).((((((((((((...((((.....................------))))..-..))))-)).......)))))).)))).))))).. ( -30.91)
>DroSim_CAF1 65332 105 + 1
GCACAGGCCGCGAAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCACCCGCCCCCUUCCCA------UGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAU
.....(((((((((....(....).((((((((((((...((((.....................------))))..-..))))-)).......)))))).)))).))))).. ( -30.91)
>DroEre_CAF1 84288 111 + 1
GCACAAGCCGCGAAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCACCCGCCCCCUGCCCCUGCUCCUGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAU
......((((((((....(....).((((((((((((...((((....((...((.....))...))....))))..-..))))-)).......)))))).)))).))))... ( -28.71)
>DroYak_CAF1 83864 99 + 1
GCACAUGCCGCGAAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCACCCGCCCCCUG------------CCCC-UUUGCA-ACCCACUUUUGGCCAAUUCGUUGGCCAU
((....)).((((((...((......(((..((.(((...(....))))))..)))....)------------)..)-))))).-.........(((((((....))))))). ( -25.70)
>DroAna_CAF1 101751 103 + 1
GCUCUGG--ACGAGGCCAGUUUACAUGGCCAGUUGGAU-GACCAGCACCCCUCUACCCCCUCAGU------GGACUGUUUUUUU-UUUUUUUUUUGGCCAAUUCGUUGGCCAU
.....((--....(((((.......))))).(((((..-..)))))...))(((((.......))------)))..........-.........(((((((....))))))). ( -29.70)
>consensus
GCACAGGCCGCGAAGCCAGUUUACAUGGCCAGUUGGACUUGGCAACUCCACCCGCCCCCUGCCCA______UGCCCC_UUUCCA_ACCCACUUUUGGCCAAUUCGUUGGCCAU
((.((((((((...((((.......))))..).))).))))))...................................................(((((((....))))))). (-21.06 = -21.32 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,619,293 – 9,619,399
Length 106
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.11
Mean single sequence MFE -38.32
Consensus MFE -24.33
Energy contribution -25.00
Covariance contribution 0.67
Combinations/Pair 1.17
Mean z-score -2.04
Structure conservation index 0.63
SVM decision value 0.27
SVM RNA-class probability 0.662510
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9619293 106 - 22224390
AUGGCCAACGAAUUGGCCAAAAGUGGGUUUGGAAA-GGGGCA------CAGGCAGGGGGCGAUUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUAAGCGGCCUAUGC
.(((((((....)))))))..(((.((((((.(..-..(((.------(((...(((((((((....))))))...)))..)))))).).)))))).)))..(((.....))) ( -36.70)
>DroSec_CAF1 79726 105 - 1
AUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCA------UGGGAAGGGGGCGGGUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUUCGCGGCCUGUGC
.(((((((....)))))))...(..(((-(((((.-((.(((------(((..((.((((...(((.....))).))))..))..))))))...))...))).)))))..).. ( -40.20)
>DroSim_CAF1 65332 105 - 1
AUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCA------UGGGAAGGGGGCGGGUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUUCGCGGCCUGUGC
.(((((((....)))))))...(..(((-(((((.-((.(((------(((..((.((((...(((.....))).))))..))..))))))...))...))).)))))..).. ( -40.20)
>DroEre_CAF1 84288 111 - 1
AUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCAGGAGCAGGGGCAGGGGGCGGGUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUUCGCGGCUUGUGC
.(((((((....)))))))...(..(((-((((..-.((.(((..(((.((.(((.((((...(((.....))).))))..))).)).)))...))).)))).)))))..).. ( -42.50)
>DroYak_CAF1 83864 99 - 1
AUGGCCAACGAAUUGGCCAAAAGUGGGU-UGCAAA-GGGG------------CAGGGGGCGGGUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUUCGCGGCAUGUGC
.(((((((....))))))).((((.(((-((((..-.((.------------(((.((((...(((.....))).))))..))).)).))).)))).))))............ ( -35.80)
>DroAna_CAF1 101751 103 - 1
AUGGCCAACGAAUUGGCCAAAAAAAAAA-AAAAAAACAGUCC------ACUGAGGGGGUAGAGGGGUGCUGGUC-AUCCAACUGGCCAUGUAAACUGGCCUCGU--CCAGAGC
.(((((((....))))))).........-.............------.((((.(((((...((..((((((((-(......)))))).)))..)).))))).)--.)))... ( -34.50)
>consensus
AUGGCCAACGAAUUGGCCAAAAGUGGGU_UGGAAA_GGGGCA______UGGGAAGGGGGCGGGUGGAGUUGCCAAGUCCAACUGGCCAUGUAAACUGGCUUCGCGGCCUGUGC
.(((((((....)))))))..................((((...............((((...(((.....))).))))....(((((.(....)))))).....)))).... (-24.33 = -25.00 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,619,329 – 9,619,437
Length 108
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -23.96
Consensus MFE -18.22
Energy contribution -18.13
Covariance contribution -0.08
Combinations/Pair 1.19
Mean z-score -1.39
Structure conservation index 0.76
SVM decision value 0.24
SVM RNA-class probability 0.649839
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9619329 108 + 22224390
ACUUGGCAACUCCAAUCGCCCCCUGCCUG------UGCCCC-UUUCCAAACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUUCG--UACUG
....((((...............)))).(------(((...-...(((((......))))).....(((.(((((((....))))))).)))..(((((....))))).)--))).. ( -24.36)
>DroSec_CAF1 79762 107 + 1
ACUUGGCAACUCCACCCGCCCCCUUCCCA------UGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUUCG--UACUU
....(((..........((..........------.))...-......-....((.(((((.....(((.(((((((....))))))).)))))))).)).)))......--..... ( -20.90)
>DroSim_CAF1 65368 107 + 1
ACUUGGCAACUCCACCCGCCCCCUUCCCA------UGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUUCG--UAGUU
....(((..........((..........------.))...-......-....((.(((((.....(((.(((((((....))))))).)))))))).)).)))......--..... ( -20.90)
>DroEre_CAF1 84324 115 + 1
ACUUGGCAACUCCACCCGCCCCCUGCCCCUGCUCCUGCCCC-UUUCCA-ACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUCCUUCUUCUU
..(((((..........((.....))....((....))...-......-...........))))).(((.(((((((....))))))).)))..(((((....)))))......... ( -24.90)
>DroYak_CAF1 83900 103 + 1
ACUUGGCAACUCCACCCGCCCCCUG------------CCCC-UUUGCA-ACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUUCUUCUACUU
....(((................((------------(...-...)))-....((.(((((.....(((.(((((((....))))))).)))))))).)).)))............. ( -23.50)
>DroAna_CAF1 101785 105 + 1
AU-GACCAGCACCCCUCUACCCCCUCAGU------GGACUGUUUUUUU-UUUUUUUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGGCGACCAAACGUCGACGUU--G--UGCUC
..-....(((((...(((((.......))------)))..........-.........(((.....(((((((((((....))))))))))))))((((....))))--)--)))). ( -29.20)
>consensus
ACUUGGCAACUCCACCCGCCCCCUGCCCA______UGCCCC_UUUCCA_ACCCACUUUUGGCCAAUUCGUUGGCCAUUUUAAUGGCCGCCGACCGAACGUCGCCGUUUCG__UACUU
....(((.((.........................................((......)).....(((..((((((....))))))..)))......)).)))............. (-18.22 = -18.13 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,619,329 – 9,619,437
Length 108
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 81.30
Mean single sequence MFE -35.13
Consensus MFE -25.33
Energy contribution -25.55
Covariance contribution 0.22
Combinations/Pair 1.17
Mean z-score -2.29
Structure conservation index 0.72
SVM decision value 0.93
SVM RNA-class probability 0.884973
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9619329 108 - 22224390
CAGUA--CGAAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGUUUGGAAA-GGGGCA------CAGGCAGGGGGCGAUUGGAGUUGCCAAGU
.....--......((((((.((((((((.(.(((.......(((((((....)))))))...(((..(((....)-))..))------).)))....).)))))))))))))).... ( -40.40)
>DroSec_CAF1 79762 107 - 1
AAGUA--CGAAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCA------UGGGAAGGGGGCGGGUGGAGUUGCCAAGU
.....--......((((((.((((.(((.(((((((....))))))......(..(((.......)))-..)...-......------.........).))).)))))))))).... ( -34.30)
>DroSim_CAF1 65368 107 - 1
AACUA--CGAAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCA------UGGGAAGGGGGCGGGUGGAGUUGCCAAGU
.....--......((((((.((((.(((.(((((((....))))))......(..(((.......)))-..)...-......------.........).))).)))))))))).... ( -34.30)
>DroEre_CAF1 84324 115 - 1
AAGAAGAAGGAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGU-UGGAAA-GGGGCAGGAGCAGGGGCAGGGGGCGGGUGGAGUUGCCAAGU
.....((..(((((....)))))..))(((((((((....))))))(((..(((.(((........((-(.....-..)))....((....))....))).)))...)))))).... ( -35.40)
>DroYak_CAF1 83900 103 - 1
AAGUAGAAGAAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGU-UGCAAA-GGGG------------CAGGGGGCGGGUGGAGUUGCCAAGU
.............((((((.((((.(((.(..(((((....(((((((....)))))))..))))).(-(((...-...)------------)))..).))).)))))))))).... ( -36.30)
>DroAna_CAF1 101785 105 - 1
GAGCA--C--AACGUCGACGUUUGGUCGCCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAAAAAAA-AAAAAAACAGUCC------ACUGAGGGGGUAGAGGGGUGCUGGUC-AU
.((((--(--..((.((((.....)))).))(((.......(((((((....))))))).........-.......(((...------.)))....)))......)))))....-.. ( -30.10)
>consensus
AAGUA__CGAAACGGCGACGUUCGGUCGGCGGCCAUUAAAAUGGCCAACGAAUUGGCCAAAAGUGGGU_UGGAAA_GGGGCA______UGGGAAGGGGGCGGGUGGAGUUGCCAAGU
.............((((((.((((.(((.(((((((....)))))).........(((....................)))................).))).)))))))))).... (-25.33 = -25.55 +   0.22)

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 11:03:13 2006