Locus 1150

Sequence ID 3L_DroMel_CAF1
Location 3,328,984 – 3,329,156
Length 172
Max. P 0.999807
window1787 window1788 window1789 window1790 window1791

overview

Window 7

Location 3,328,984 – 3,329,098
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.82
Mean single sequence MFE -29.22
Consensus MFE -21.03
Energy contribution -21.51
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.72
SVM decision value 0.44
SVM RNA-class probability 0.737023
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3328984 114 + 23771897
CAUAGAGUUAGUGGGAGAAGAGGGGACUUUGAGACCCUUUGGGAAG------AACCCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCG
(((((((.((((((((((.(((((..(((.....(((...))))))------..)))))..))))))......(((........)))...)))).))))))).(((((....)))))... ( -33.60)
>DroSec_CAF1 16914 114 + 1
CAUAGAGUUAGUGGGAGAAGAGGGGACUUUGGGAACCUUUGGGAAU------AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCG
..............(((((((((((.((((((((..(((.((((..------...........)))).....)))...)))).(((....)))..........)))).))))))))))). ( -31.92)
>DroSim_CAF1 9678 113 + 1
CAUAGAGUUUGUGGGAGAAGAGGGGACUUUGGGAACCU-UGGGAAG------AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCG
(((((...))))).(((((((((((.((((((((..((-((..(((------(............))))..))))...)))).(((....)))..........)))).))))))))))). ( -35.40)
>DroEre_CAF1 17308 105 + 1
UAUAGGCUACGUAAGAAAAGCGAGAGCUUUGGGAACCUUUU-AA--------AAACCUCGACUACUCUUAAUAAGCCAUCCCAAGCU------AUUUUUAUGCGAAGACCUCUCUUUUCG
...(((((.((((.(((((.....(((((.((((..(((((-((--------...............)))).)))...)))))))))------.))))).)))).)).)))......... ( -20.36)
>DroYak_CAF1 12284 108 + 1
UGUAGGCUAAGAUGGAAAAGAGA-AGCUUUGGGA-CCUUUU-AAAGAAAAAAAAACUUCACUU---AAUAAUAAGCCAUCCCAAGCU------AUUUUUAUGCGAAGAGCUCUCUUUUCG
..............(((((((((-(((((.((((-......-...(((........))).(((---(....))))...)))))))))------........((.....))))))))))). ( -24.80)
>consensus
CAUAGAGUUAGUGGGAGAAGAGGGGACUUUGGGAACCUUUGGGAAG______AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCG
..............(((((((((((.((((((((..(((.................................)))...))))..((...............)))))).))))))))))). (-21.03 = -21.51 +   0.48)

alignment

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secondary structure

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Window 8

Location 3,328,984 – 3,329,098
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.82
Mean single sequence MFE -29.37
Consensus MFE -17.13
Energy contribution -16.65
Covariance contribution -0.48
Combinations/Pair 1.24
Mean z-score -1.73
Structure conservation index 0.58
SVM decision value 0.04
SVM RNA-class probability 0.552352
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3328984 114 - 23771897
CGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGGUU------CUUCCCAAAGGGUCUCAAAGUCCCCUCUUCUCCCACUAACUCUAUG
.((((((((.((.(((.((........(((....))).......)).........((((((..(((..------...)))....)))))).))).)).)))))))).............. ( -32.66)
>DroSec_CAF1 16914 114 - 1
CGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU------AUUCCCAAAGGUUCCCAAAGUCCCCUCUUCUCCCACUAACUCUAUG
.((((((((.((.(((............((....))((((((.(((((.....((....)).))))).------..)))))).........))).)).)))))))).............. ( -29.00)
>DroSim_CAF1 9678 113 - 1
CGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU------CUUCCCA-AGGUUCCCAAAGUCCCCUCUUCUCCCACAAACUCUAUG
.((((((((.((.(((...........(((....)))(((((..((((.....(((((((....))))------)))....-)))))))))))).)).)))))))).............. ( -32.60)
>DroEre_CAF1 17308 105 - 1
CGAAAAGAGAGGUCUUCGCAUAAAAAU------AGCUUGGGAUGGCUUAUUAAGAGUAGUCGAGGUUU--------UU-AAAAGGUUCCCAAAGCUCUCGCUUUUCUUACGUAGCCUAUA
.((((((.(((((....))........------(((((((((..((((.(((((((.........)))--------))-)).)))))))).)))))))).)))))).............. ( -23.70)
>DroYak_CAF1 12284 108 - 1
CGAAAAGAGAGCUCUUCGCAUAAAAAU------AGCUUGGGAUGGCUUAUUAUU---AAGUGAAGUUUUUUUUUCUUU-AAAAGG-UCCCAAAGCU-UCUCUUUUCCAUCUUAGCCUACA
.(((((((((((.....))........------((((((((((.(((((....)---))))((((......))))...-.....)-)))).)))))-))))))))).............. ( -28.90)
>consensus
CGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU______CUUCCCAAAGGUUCCCAAAGUCCCCUCUUCUCCCACUAACUCUAUG
.((((((((.((.(((((...............((((......)))).............)))))..................((...)).....)).)))))))).............. (-17.13 = -16.65 +  -0.48)

alignment

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secondary structure

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Window 9

Location 3,329,024 – 3,329,124
Length 100
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 83.87
Mean single sequence MFE -22.62
Consensus MFE -17.12
Energy contribution -17.60
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.94
Structure conservation index 0.76
SVM decision value 0.73
SVM RNA-class probability 0.834070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3329024 100 + 23771897
GGGAAG------AACCCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAG
..((((------(.(((((((.............((.......(((....)))........))(((((....)))))))))))).)))))................ ( -26.86)
>DroSec_CAF1 16954 100 + 1
GGGAAU------AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAG
......------....(((((.((.(((......((.......(((....)))........))(((((.(((((.....))))).)))))))).))...))))).. ( -23.16)
>DroSim_CAF1 9717 100 + 1
GGGAAG------AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAG
..((((------(..((((((.............((.......(((....)))........))(((((....)))))))))))..)))))................ ( -24.66)
>DroEre_CAF1 17348 91 + 1
U-AA--------AAACCUCGACUACUCUUAAUAAGCCAUCCCAAGCU------AUUUUUAUGCGAAGACCUCUCUUUUCGAGGGCUCUUCAAAAACCACUCGACAG
.-..--------.....((((............(((........)))------..........(((((.(((((.....))))).))))).........))))... ( -16.80)
>DroYak_CAF1 12322 96 + 1
U-AAAGAAAAAAAAACUUCACUU---AAUAAUAAGCCAUCCCAAGCU------AUUUUUAUGCGAAGAGCUCUCUUUUCGAGGGCUCUUCAAAAACCACUCGAGAG
.-...(((........))).(((---.......(((........)))------..........(((((((((((.....)))))))))))...........))).. ( -21.60)
>consensus
GGGAAG______AAACCUCGAUCUCUCUUAAUAAGCCAUCCCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAG
................(((((............(((........)))................(((((.(((((.....))))).))))).........))))).. (-17.12 = -17.60 +   0.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,329,024 – 3,329,124
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.87
Mean single sequence MFE -29.22
Consensus MFE -19.64
Energy contribution -21.56
Covariance contribution 1.92
Combinations/Pair 1.08
Mean z-score -2.12
Structure conservation index 0.67
SVM decision value 0.63
SVM RNA-class probability 0.806086
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3329024 100 - 23771897
CUCUCGAGUGCUUUCUGAAGAGCCCUCGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGGUU------CUUCCC
(((((((...(((((((((((.(((((.....))).)))))))((........(((....))).......))......)))))).)))))))..------...... ( -32.46)
>DroSec_CAF1 16954 100 - 1
CUCUCGAGUGCUUUCUGAAGAGCCCUCGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU------AUUCCC
.((((((...(((((((((((.(((((.....))).)))))))((........(((....))).......))......)))))).))))))...------...... ( -29.96)
>DroSim_CAF1 9717 100 - 1
CUCUCGAGUGCUUUCUGAAGAGCCCUCGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU------CUUCCC
.((((((...(((((((((((.(((((.....))).)))))))((........(((....))).......))......)))))).))))))...------...... ( -29.96)
>DroEre_CAF1 17348 91 - 1
CUGUCGAGUGGUUUUUGAAGAGCCCUCGAAAAGAGAGGUCUUCGCAUAAAAAU------AGCUUGGGAUGGCUUAUUAAGAGUAGUCGAGGUUU--------UU-A
...((((((.(((((((((((.(((((.....))).)))))))....))))))------.))))))(((.((((.....)))).))).......--------..-. ( -23.20)
>DroYak_CAF1 12322 96 - 1
CUCUCGAGUGGUUUUUGAAGAGCCCUCGAAAAGAGAGCUCUUCGCAUAAAAAU------AGCUUGGGAUGGCUUAUUAUU---AAGUGAAGUUUUUUUUUCUUU-A
.((((((((.(((((((((((((.(((.....))).)))))))....))))))------.))))))))..(((((....)---))))((((......))))...-. ( -30.50)
>consensus
CUCUCGAGUGCUUUCUGAAGAGCCCUCGAGAAGAGAGGUCUUCGCAUAAAAAUAGCAAUAGCUUGGGAUGGCUUAUUAAGAGAGAUCGAGGUUU______CUUCCC
.((((((...(((((((((((.(.(((.....))).).)))))................((((......)))).....)))))).))))))............... (-19.64 = -21.56 +   1.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,329,058 – 3,329,156
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -25.82
Consensus MFE -22.30
Energy contribution -22.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.25
Structure conservation index 0.86
SVM decision value 4.13
SVM RNA-class probability 0.999807
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3329058 98 + 23771897
CCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAGUAAAAUUAUGCAUGAAAUGUUUGCAC--ACAAAA
....((....((...(((((((((.(((....)))(((((((.(((........))).))))))).........))))))))).))..))..--...... ( -24.60)
>DroSec_CAF1 16988 98 + 1
CCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAGUAAAAUUAUGCAUGAAAUGUUUGCAC--ACAAAA
....((....((...(((((((((.(((....)))(((((((.(((........))).))))))).........))))))))).))..))..--...... ( -24.60)
>DroSim_CAF1 9751 98 + 1
CCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAGUAAAAUUAUGCAUGAAAUGUUUGCAC--ACAAAA
....((....((...(((((((((.(((....)))(((((((.(((........))).))))))).........))))))))).))..))..--...... ( -24.60)
>DroEre_CAF1 17379 92 + 1
CCAAGCU------AUUUUUAUGCGAAGACCUCUCUUUUCGAGGGCUCUUCAAAAACCACUCGACAGUAAAAUUAUGCAUGAAAUGUUUGCAC--ACAAAA
.(((((.------..(((((((((((((.(((((.....))))).))))).......(((....)))........)))))))).)))))...--...... ( -24.50)
>DroYak_CAF1 12358 94 + 1
CCAAGCU------AUUUUUAUGCGAAGAGCUCUCUUUUCGAGGGCUCUUCAAAAACCACUCGAGAGUAAAAUUAUGCAUGAAACGUUUGCACACACAAAA
.(((((.------..(((((((((((((((((((.....))))))))))).......(((....)))........)))))))).)))))........... ( -30.80)
>consensus
CCAAGCUAUUGCUAUUUUUAUGCGAAGACCUCUCUUCUCGAGGGCUCUUCAGAAAGCACUCGAGAGUAAAAUUAUGCAUGAAAUGUUUGCAC__ACAAAA
.(((((.........(((((((((((((.(((((.....))))).))))).......(((....)))........)))))))).)))))........... (-22.30 = -22.30 +   0.00)

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 10:00:25 2006