Locus 2707

Sequence ID X_DroMel_CAF1
Location 7,262,541 – 7,262,680
Length 139
Max. P 0.891976
window4429 window4430 window4431

overview

Window 9

Location 7,262,541 – 7,262,655
Length 114
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.84
Mean single sequence MFE -42.03
Consensus MFE -28.41
Energy contribution -30.67
Covariance contribution 2.25
Combinations/Pair 1.17
Mean z-score -1.70
Structure conservation index 0.68
SVM decision value 0.97
SVM RNA-class probability 0.891976
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7262541 114 + 22224390
CUUGUGUCCUAUUUAUGGGUCAGAGCUGCUUGGCGGCUCCCUCGGCCGAUGAUUUGGCCAAAUUUGGUGAAAUGGAACGUUCCAUCAAGGAGCUGACCAGUUCGAUCCUGGCCA
................(((((.((((((.....(((((((...((((((....))))))....((((((.((((...)))).)))))))))))))..)))))))))))...... ( -42.20)
>DroPse_CAF1 39509 114 + 1
CUCUAUUUUUGUGCUUGACCCAGAACUGCUGGGCGGCUCCCUCCGGCGAUGAUUUGGCCAAGCUCGGAGAACUGGAGCGCACCAUCAAGGAGCUGACCAGCUCGAUACUGACCA
..........((((.((.(((((.....)))))))((((((((((((..((.......)).)).)))))....))))))))).......(((((....)))))........... ( -39.00)
>DroSim_CAF1 11223 114 + 1
CUUGUAUCCUAUUUAUGGGCCAGAAUUGCUUGGCGGCUCCCUCGGCCGAUGAUUUGGCCAAAUUUGGUGAAAUGGAACGUUCCAUCAAGGAGCUGACCAGUUCGAUCCUGGCCA
.................((((((.((((.(((((((((((...((((((....))))))....((((((.((((...)))).))))))))))))).))))..)))).)))))). ( -47.90)
>DroYak_CAF1 37212 114 + 1
UUUGUAUCCUGUUUAUGGGUCAGCAUUGUUGGGCAGCUUCAUCGGCCGAUGAUUUGGCCAAAUUCGGGGAAAUGGAACGAUCCAUCAAGGAGCUGACCAGUUCGAUCCUGGCCA
.................((((((.((((((((.(((((((...((((((....))))))............(((((....)))))...))))))).))))..)))).)))))). ( -41.70)
>DroAna_CAF1 14769 114 + 1
UAUUGGCCCUGUGCCUGGGCCACAGUGUGUGGGCAGCUCCCUCGGCGGAGGACCUGGCCCAGUUCGGGGAGCUGGAGAAAACCAUCAAGGAGCUAACCAACUCGAUCUUGGCCA
....((.(((.((((.(((((((.....))))......)))..)))).))).)).((((.((.(((((..(.(((......))).)..((......))..))))).)).)))). ( -42.40)
>DroPer_CAF1 66055 114 + 1
CUCUAUUUUUGUGCUUGACCCAGAACUGCUGGGCGGCUCCCUCCGGCGAUGAUUUGGCCAAGCUCGGAGAACUGGAGCGCACCAUCAAGGAGCUGACCAGCUCGAUACUGACCA
..........((((.((.(((((.....)))))))((((((((((((..((.......)).)).)))))....))))))))).......(((((....)))))........... ( -39.00)
>consensus
CUUGUAUCCUGUGCAUGGGCCAGAACUGCUGGGCGGCUCCCUCGGCCGAUGAUUUGGCCAAAUUCGGAGAAAUGGAACGAACCAUCAAGGAGCUGACCAGCUCGAUCCUGGCCA
.................((((((....(((((.(((((((...((((((....)))))).........((..(((......)))))..))))))).)))))......)))))). (-28.41 = -30.67 +   2.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,262,541 – 7,262,655
Length 114
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.84
Mean single sequence MFE -40.15
Consensus MFE -23.02
Energy contribution -23.55
Covariance contribution 0.53
Combinations/Pair 1.18
Mean z-score -1.71
Structure conservation index 0.57
SVM decision value 0.32
SVM RNA-class probability 0.688935
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7262541 114 - 22224390
UGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGUUCCAUUUCACCAAAUUUGGCCAAAUCAUCGGCCGAGGGAGCCGCCAAGCAGCUCUGACCCAUAAAUAGGACACAAG
(((((((.......)))))))(.((((..((((...................(((((((........)))))))(((((.((...)).)))))...))))....)))))..... ( -36.90)
>DroPse_CAF1 39509 114 - 1
UGGUCAGUAUCGAGCUGGUCAGCUCCUUGAUGGUGCGCUCCAGUUCUCCGAGCUUGGCCAAAUCAUCGCCGGAGGGAGCCGCCCAGCAGUUCUGGGUCAAGCACAAAAAUAGAG
((..((((.....))))..)).(((..(....(((((((((....(((((.((.(((.....)))..)))))))))))).((((((.....))))))...))))....)..))) ( -41.70)
>DroSim_CAF1 11223 114 - 1
UGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGUUCCAUUUCACCAAAUUUGGCCAAAUCAUCGGCCGAGGGAGCCGCCAAGCAAUUCUGGCCCAUAAAUAGGAUACAAG
.(((((((((.(...((((..(((((((((((((....))))))..........(((((........)))))))))))).))))..).)))))))))................. ( -43.20)
>DroYak_CAF1 37212 114 - 1
UGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAUCGUUCCAUUUCCCCGAAUUUGGCCAAAUCAUCGGCCGAUGAAGCUGCCCAACAAUGCUGACCCAUAAACAGGAUACAAA
(((((((.......)))))))..((((..((((.((.................((((((........))))))...(((...........))))).))))....))))...... ( -30.30)
>DroAna_CAF1 14769 114 - 1
UGGCCAAGAUCGAGUUGGUUAGCUCCUUGAUGGUUUUCUCCAGCUCCCCGAACUGGGCCAGGUCCUCCGCCGAGGGAGCUGCCCACACACUGUGGCCCAGGCACAGGGCCAAUA
(((((.((.(((((((((..((..((.....))..))..)))))))...)).)).)))))((((((..(((..(((......((((.....))))))).)))..)))))).... ( -47.10)
>DroPer_CAF1 66055 114 - 1
UGGUCAGUAUCGAGCUGGUCAGCUCCUUGAUGGUGCGCUCCAGUUCUCCGAGCUUGGCCAAAUCAUCGCCGGAGGGAGCCGCCCAGCAGUUCUGGGUCAAGCACAAAAAUAGAG
((..((((.....))))..)).(((..(....(((((((((....(((((.((.(((.....)))..)))))))))))).((((((.....))))))...))))....)..))) ( -41.70)
>consensus
UGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGCUCCAGUUCACCGAACUUGGCCAAAUCAUCGGCCGAGGGAGCCGCCCAGCAAUUCUGGCCCAUAAACAGGAAAAAAG
(((((((.......)))))))(((((....(((......)))..........(((((((........))))))))))))................................... (-23.02 = -23.55 +   0.53)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,262,575 – 7,262,680
Length 105
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 80.65
Mean single sequence MFE -39.12
Consensus MFE -24.07
Energy contribution -25.43
Covariance contribution 1.36
Combinations/Pair 1.12
Mean z-score -1.94
Structure conservation index 0.62
SVM decision value 0.43
SVM RNA-class probability 0.734920
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7262575 105 - 22224390
-AACCUACCGGUAG------UAGCUCCACUCAUGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGUUCCAUUUCACCAAAUUUGGCCAAAUCAUCGGCCGAGGGAGCC
-.(((....)))..------..(((((.(((.(((((((.......))))))).......((((((....))))))...........((((........)))))))))))). ( -38.00)
>DroPse_CAF1 39543 112 - 1
GGACUCACCUGCUCCUGCUCCUCCUGCACUCAUGGUCAGUAUCGAGCUGGUCAGCUCCUUGAUGGUGCGCUCCAGUUCUCCGAGCUUGGCCAAAUCAUCGCCGGAGGGAGCC
((.(((....((....)).(((((.((.....(((((((..(((((((((...((.((.....)).))...)))))))...))..))))))).......)).)))))))))) ( -41.90)
>DroSim_CAF1 11257 105 - 1
-AACGUACCGGGAG------UAGCUCCACUCAUGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGUUCCAUUUCACCAAAUUUGGCCAAAUCAUCGGCCGAGGGAGCC
-.........((((------...)))).....(((((((.......)))))))(((((((((((((....))))))..........(((((........)))))))))))). ( -37.90)
>DroEre_CAF1 22387 105 - 1
-GGCCUACCGGCAG------UGGCUCCACUCAGGGCCAGGAUCGAACUGGCCAGCUCCCUGAUGGAUCGUUCCAUUUCCCCAAACUUGGCCAAAUCAUCGGCCGACGGUGCU
-.(((....)))((------((....))))...((((((.......))))))(((.((..((((((....)))))).........((((((........)))))).)).))) ( -39.80)
>DroYak_CAF1 37246 105 - 1
-AACGCACCGGGAG------UAGCUCCACUCAUGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAUCGUUCCAUUUCCCCGAAUUUGGCCAAAUCAUCGGCCGAUGAAGCU
-...((..((((((------.((((........((((((.......)))))))))).)).((((((....))))))..))))...((((((........))))))....)). ( -35.20)
>DroPer_CAF1 66089 112 - 1
GGACUCACCUGCUCCUGCUCCUCCUGCACUCAUGGUCAGUAUCGAGCUGGUCAGCUCCUUGAUGGUGCGCUCCAGUUCUCCGAGCUUGGCCAAAUCAUCGCCGGAGGGAGCC
((.(((....((....)).(((((.((.....(((((((..(((((((((...((.((.....)).))...)))))))...))..))))))).......)).)))))))))) ( -41.90)
>consensus
_AACCCACCGGCAG______UAGCUCCACUCAUGGCCAGGAUCGAACUGGUCAGCUCCUUGAUGGAACGUUCCAUUUCACCAAACUUGGCCAAAUCAUCGGCCGAGGGAGCC
................................(((((((.......)))))))(((((..(((((......)))))........(((((((........)))))))))))). (-24.07 = -25.43 +   1.36)

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 10:41:24 2006