Locus 7128

Sequence ID X_DroMel_CAF1
Location 17,888,022 – 17,888,180
Length 158
Max. P 0.998077
window11641 window11642 window11643 window11644

overview

Window 1

Location 17,888,022 – 17,888,140
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.77
Mean single sequence MFE -22.46
Consensus MFE -18.16
Energy contribution -18.44
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -2.50
Structure conservation index 0.81
SVM decision value 2.06
SVM RNA-class probability 0.986903
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17888022 118 + 22224390
--UUAAUUUAAAGCAACCGCUUUUAAUAAUCACCAUUUAUUGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUUUG
--...(((.(((((....))))).))).....................((((((((((.((....(((((....))))).......(((....)))))...))))))))))......... ( -23.30)
>DroSec_CAF1 151999 118 + 1
--UUAAUUUAAAGCAACCGCUUUUAAUAAUCACCAUUUAUUGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUAAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUG
--...(((.(((((....))))).))).....................((((((((((((((...............................)))))....)))))))))......... ( -19.88)
>DroSim_CAF1 130705 118 + 1
--UUAAUUUAAAGCAACCGCUUUUAAUAAUCACCAUUUAUUGCAACUCGCAAACUGCUCUCAGCGAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUG
--...(((.(((((....))))).))).....................((((((((((.((.(.((((((....))))))).....(((....)))))...))))))))))......... ( -27.20)
>DroEre_CAF1 147864 120 + 1
UAUUAAUUUAAAGCACACGCUUUUAAUAAUCACCAUUUAUUGCAACUUGCGAAAUGCUCUCAGGAAAUUUACAUGAAUUUCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUG
..........(((((.((((((((.........((((..((((.....)))))))).(((((.(((((((....)))))))............))))))))))).)).)))))....... ( -22.12)
>DroYak_CAF1 148370 118 + 1
--AUAAUUUAAAGCACCCGCUUUUAAUAAUCACCAUUUAUUGCAACUUGCAAAAUGCUCUCAGCAAAUUUACAUGAAUUCCAAUUAACAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUG
--........(((((..(((((((.....(((.......((((.....))))..(((.....)))........))).(((((...........))))))))))).)..)))))....... ( -19.80)
>consensus
__UUAAUUUAAAGCAACCGCUUUUAAUAAUCACCAUUUAUUGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUG
.....(((.(((((....))))).))).....................((((((((((.(((...........))).(((((...........)))))...))))))))))......... (-18.16 = -18.44 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,888,022 – 17,888,140
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.77
Mean single sequence MFE -29.31
Consensus MFE -25.26
Energy contribution -25.90
Covariance contribution 0.64
Combinations/Pair 1.12
Mean z-score -2.41
Structure conservation index 0.86
SVM decision value 3.00
SVM RNA-class probability 0.998077
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17888022 118 - 22224390
CAAAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGGUUGCUUUAAAUUAA--
..((((((((((((((((((((..(((....)))......((((((....))))))...))))))))))))).(((..(........)..)))...........))))))).......-- ( -31.70)
>DroSec_CAF1 151999 118 - 1
CAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUUAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGGUUGCUUUAAAUUAA--
..((((((((((((((((((((..(((....)))......((((((....))))))...))))))))))))).(((..(........)..)))...........))))))).......-- ( -29.70)
>DroSim_CAF1 130705 118 - 1
CAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUCGCUGAGAGCAGUUUGCGAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGGUUGCUUUAAAUUAA--
..((((((((((((((((((((..(((....)))......((((((....))))))...))))))))))))).(((..(........)..)))...........))))))).......-- ( -34.30)
>DroEre_CAF1 147864 120 - 1
CAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGAAAUUCAUGUAAAUUUCCUGAGAGCAUUUCGCAAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGUGUGCUUUAAAUUAAUA
.......(((((.((.((((((((((((.....((((((((((((......))))))......((.....)).)))))).....)))).)).....)))))))).))))).......... ( -22.20)
>DroYak_CAF1 148370 118 - 1
CAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGUUAAUUGGAAUUCAUGUAAAUUUGCUGAGAGCAUUUUGCAAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGGGUGCUUUAAAUUAU--
.......(((((..((((((((.......((..((.((((.((((..((((((..(((.....))).)))))))))).)))).))..)).......)))))))).)))))........-- ( -28.64)
>consensus
CAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCAAUAAAUGGUGAUUAUUAAAAGCGGUUGCUUUAAAUUAA__
..((((((.(((((((((((((..(((....)))......((((((....))))))...))))))))))))).(((..(........)..)))............))))))......... (-25.26 = -25.90 +   0.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,888,060 – 17,888,180
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -26.54
Consensus MFE -20.66
Energy contribution -21.94
Covariance contribution 1.28
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.78
SVM decision value 0.61
SVM RNA-class probability 0.798473
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17888060 120 + 22224390
UGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUUUGGCAAAAUUGUUGCUAAAAUGUGUAAAAACAAACUGUUGUG
.(((((..((((((((((.((....(((((....))))).......(((....)))))...)))))))))).((((((((((((.....))))))))).)))............))))). ( -32.80)
>DroSec_CAF1 152037 120 + 1
UGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUAAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUGGCCAAAUUGUUGCUAAAAUGUGUAAAACCAAACUGUUGUG
.(((((..((((((((((((((...............................)))))....))))))))).(((((.((((.........)))).)).)))............))))). ( -22.58)
>DroSim_CAF1 130743 120 + 1
UGCAACUCGCAAACUGCUCUCAGCGAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUGGCCAAAUUGUUGCUAAAAUGUGUAAAACCAAACUGUGUUG
..((((.(((((((((((.((.(.((((((....))))))).....(((....)))))...)))))))))).(((((.((((.........)))).)).)))............).)))) ( -28.00)
>DroEre_CAF1 147904 120 + 1
UGCAACUUGCGAAAUGCUCUCAGGAAAUUUACAUGAAUUUCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUGGCAAAAAUGUUGCUAAAAUGUGUAAAAACAAACUGUUGUG
.(((((..(((((.((((.((..(((((((....))))))).....(((....)))))...)))).))))).(((((.((((((.....)))))).)).)))............))))). ( -25.40)
>DroYak_CAF1 148408 120 + 1
UGCAACUUGCAAAAUGCUCUCAGCAAAUUUACAUGAAUUCCAAUUAACAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUGGCAAAAUUGUUGCUUAAAUGUGUAAAAACAAACUGUUGUG
.(((((........(((.....)))..(((((((...(((((...........)))))..((((((((((((.......))))))....))))))....)))))))........))))). ( -23.90)
>consensus
UGCAACUCGCAAACUGCUCUCAGCAAAUUCAUAUGAAUUCCAAUUACCAAUUAUGGGAAAAAGCAGUUUGCUUACUUCUGGCAAAAUUGUUGCUAAAAUGUGUAAAAACAAACUGUUGUG
.(((((..((((((((((.(((...........))).(((((...........)))))...)))))))))).(((((.((((((.....)))))).)).)))............))))). (-20.66 = -21.94 +   1.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,888,060 – 17,888,180
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -28.76
Consensus MFE -25.66
Energy contribution -26.86
Covariance contribution 1.20
Combinations/Pair 1.10
Mean z-score -2.11
Structure conservation index 0.89
SVM decision value 2.91
SVM RNA-class probability 0.997689
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17888060 120 - 22224390
CACAACAGUUUGUUUUUACACAUUUUAGCAACAAUUUUGCCAAAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCA
...........................(((((....((((.....))))(((((((((((((..(((....)))......((((((....))))))...)))))))))))))..))))). ( -32.80)
>DroSec_CAF1 152037 120 - 1
CACAACAGUUUGGUUUUACACAUUUUAGCAACAAUUUGGCCAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUUAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCA
..((((..(((((((......................))))))).....(((((((((((((..(((....)))......((((((....))))))...)))))))))))))..)))).. ( -29.95)
>DroSim_CAF1 130743 120 - 1
CAACACAGUUUGGUUUUACACAUUUUAGCAACAAUUUGGCCAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUCGCUGAGAGCAGUUUGCGAGUUGCA
((((....(((((((......................))))))).....(((((((((((((..(((....)))......((((((....))))))...)))))))))))))..)))).. ( -34.05)
>DroEre_CAF1 147904 120 - 1
CACAACAGUUUGUUUUUACACAUUUUAGCAACAUUUUUGCCAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGAAAUUCAUGUAAAUUUCCUGAGAGCAUUUCGCAAGUUGCA
..(((((((((((((....((.((((.((((.....)))).)))))))))))))))((((((..(((....))).....((((((......))))))..)))))).........)))).. ( -23.90)
>DroYak_CAF1 148408 120 - 1
CACAACAGUUUGUUUUUACACAUUUAAGCAACAAUUUUGCCAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGUUAAUUGGAAUUCAUGUAAAUUUGCUGAGAGCAUUUUGCAAGUUGCA
..((((................(((((..(((((((.((...((((.((((.....)))))))).)).)))))))..))))).....((((((..(((.....))).)))))).)))).. ( -23.10)
>consensus
CACAACAGUUUGUUUUUACACAUUUUAGCAACAAUUUUGCCAGAAGUAAGCAAACUGCUUUUUCCCAUAAUUGGUAAUUGGAAUUCAUAUGAAUUUGCUGAGAGCAGUUUGCGAGUUGCA
...........................(((((....((((.....))))(((((((((((((..(((....)))......((((((....))))))...)))))))))))))..))))). (-25.66 = -26.86 +   1.20)

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 12:30:52 2006