Locus 7181

Sequence ID 3L_DroMel_CAF1
Location 19,253,326 – 19,253,467
Length 141
Max. P 0.973625
window11661 window11662 window11663 window11664

overview

Window 1

Location 19,253,326 – 19,253,427
Length 101
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 63.70
Mean single sequence MFE -25.73
Consensus MFE -12.80
Energy contribution -13.05
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.50
SVM decision value 0.93
SVM RNA-class probability 0.883456
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19253326 101 + 23771897
GCUAGCUGUUCACACC----ACUUAA-------GUAGUUCGAUUGGAUGUUUCCAGGCCCACCGACUACUAGGCACUAUGCCUAGGAUUCAAUGCCGGUCA---CCGGCUUAUCA
..............((----......-------((((((....((((....))))((....))))))))(((((.....))))))).......(((((...---)))))...... ( -27.10)
>DroSim_CAF1 88076 90 + 1
N----NNNNN-----N----NNNNNN-------NNNNNNNNNNNNNNNNNNNCCAGGCCCACCGACUACUGGGCACUAUGG-----CUUCAAUGCCGGUCACCACCGGCUUAUCA
.----.....-----.----......-------...................(((.(((((........)))))....)))-----.......((((((....))))))...... ( -21.00)
>DroEre_CAF1 85940 95 + 1
G----CUGUUCGCACC----ACUACAGUAGUUAGUAGUUCGAUUAGAUGUUUCCAGGCCUACCGACU----GGCACUAUGG-----UUUCAAUGCCGGUCA---CCGGCUUAUCA
.----(((.(((.((.----((((.......)))).)).))).)))........(((((....((((----((((...((.-----...)).)))))))).---..))))).... ( -25.10)
>DroYak_CAF1 112378 92 + 1
G----CUGUUCACACGUCGAACUAAA-------GCAGUUCGAUUAGAUGUUUCCAGGCCUACCGACU----GGCACUGUGG-----UUUCAAUGCCGGUCA---CCGGCUUAUCA
.----(((...(((.((((((((...-------..))))))))....)))...)))(((....((((----((((.((...-----...)).)))))))).---..)))...... ( -29.70)
>consensus
G____CUGUUCACACC____ACUAAA_______GUAGUUCGAUUAGAUGUUUCCAGGCCCACCGACU____GGCACUAUGG_____UUUCAAUGCCGGUCA___CCGGCUUAUCA
....................................................(((.(((............)))....)))............(((((......)))))...... (-12.80 = -13.05 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,253,326 – 19,253,427
Length 101
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 63.70
Mean single sequence MFE -29.40
Consensus MFE -15.73
Energy contribution -16.48
Covariance contribution 0.75
Combinations/Pair 1.15
Mean z-score -1.82
Structure conservation index 0.53
SVM decision value 1.71
SVM RNA-class probability 0.973625
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19253326 101 - 23771897
UGAUAAGCCGG---UGACCGGCAUUGAAUCCUAGGCAUAGUGCCUAGUAGUCGGUGGGCCUGGAAACAUCCAAUCGAACUAC-------UUAAGU----GGUGUGAACAGCUAGC
......(((((---...)))))(((((...((((((.....))))))...))))).(((.((((....)))).(((.(((((-------....))----))).)))...)))... ( -33.30)
>DroSim_CAF1 88076 90 - 1
UGAUAAGCCGGUGGUGACCGGCAUUGAAG-----CCAUAGUGCCCAGUAGUCGGUGGGCCUGGNNNNNNNNNNNNNNNNNNN-------NNNNNN----N-----NNNNN----N
......((((((....)))))).......-----...(((.(((((.(....).))))))))....................-------......----.-----.....----. ( -22.00)
>DroEre_CAF1 85940 95 - 1
UGAUAAGCCGG---UGACCGGCAUUGAAA-----CCAUAGUGCC----AGUCGGUAGGCCUGGAAACAUCUAAUCGAACUACUAACUACUGUAGU----GGUGCGAACAG----C
......(((..---((((.(((((((...-----...)))))))----.))))...))).((....)).....(((.(((((((.(....)))))----))).)))....----. ( -29.70)
>DroYak_CAF1 112378 92 - 1
UGAUAAGCCGG---UGACCGGCAUUGAAA-----CCACAGUGCC----AGUCGGUAGGCCUGGAAACAUCUAAUCGAACUGC-------UUUAGUUCGACGUGUGAACAG----C
......(((..---((((.(((((((...-----...)))))))----.))))...)))(((...((((....((((((((.-------..)))))))).))))...)))----. ( -32.60)
>consensus
UGAUAAGCCGG___UGACCGGCAUUGAAA_____CCAUAGUGCC____AGUCGGUAGGCCUGGAAACAUCUAAUCGAACUAC_______UUUAGU____GGUGUGAACAG____C
......(((((......)))))...............(((.(((((........))))))))..................................................... (-15.73 = -16.48 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,253,353 – 19,253,467
Length 114
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 78.05
Mean single sequence MFE -32.75
Consensus MFE -21.94
Energy contribution -22.33
Covariance contribution 0.39
Combinations/Pair 1.08
Mean z-score -1.44
Structure conservation index 0.67
SVM decision value 0.50
SVM RNA-class probability 0.761966
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19253353 114 + 23771897
UCGAUUGGAUGUUUCCAGGCCCACCGACUACUAGGCACUAUGCCUAGGAUUCAAUGCCGGUCA---CCGGCUUAUCACCUGAACCACACAUGAUAUUUGCCACUGGGCGAUGGGUGG
....(((((....)))))..(((((((...((((((.....))))))...))...(((((...---))))).(((((..((.....))..))))).(((((....)))))..))))) ( -39.20)
>DroPse_CAF1 25527 94 + 1
UCGAUUAGAUGUUUCUAGGCCUACU-AUU----AGCAUU---------------UGCCGGUCG---CCGGCUUAUCACCUGAACUACACAUGAUAUUUGCGAGUGGGCGAUGAGUUC
(((.(((((....)))))(((((((-...----.(((..---------------.(((((...---))))).(((((..((.....))..)))))..))).)))))))..))).... ( -28.30)
>DroSim_CAF1 88094 112 + 1
NNNNNNNNNNNNNNCCAGGCCCACCGACUACUGGGCACUAUGG-----CUUCAAUGCCGGUCACCACCGGCUUAUCACCUGAACCACACAUGAUAUUUGCCACUGGGCGAUGGUUGG
..............(((((((((........)))))....(((-----(......((((((....)))))).(((((..((.....))..)))))...))))))))........... ( -33.00)
>DroEre_CAF1 85970 105 + 1
UCGAUUAGAUGUUUCCAGGCCUACCGACU----GGCACUAUGG-----UUUCAAUGCCGGUCA---CCGGCUUAUCACCUGCACCACACAUGAUAUUUGCCACUGGGCGAUGGGUGG
.............((((.(((((..((((----((((...((.-----...)).)))))))).---..(((.(((((..((.....))..)))))...)))..)))))..))))... ( -32.40)
>DroYak_CAF1 112405 105 + 1
UCGAUUAGAUGUUUCCAGGCCUACCGACU----GGCACUGUGG-----UUUCAAUGCCGGUCA---CCGGCUUAUCACCUGAACCACACAUGAUAUUUGCCACUGGGCGAUGGGUGG
.............((((.(((((..((((----((((.((...-----...)).)))))))).---..(((.(((((..((.....))..)))))...)))..)))))..))))... ( -35.30)
>DroPer_CAF1 25464 94 + 1
UCGAUUAGAUGUUUCUAGGCCUACU-AUU----AGCAUU---------------UGCCGGUCG---CCGGCUUAUCACCUGAACUACACAUGAUAUUUGCGAGUGGGCGAUGAGUUC
(((.(((((....)))))(((((((-...----.(((..---------------.(((((...---))))).(((((..((.....))..)))))..))).)))))))..))).... ( -28.30)
>consensus
UCGAUUAGAUGUUUCCAGGCCUACCGACU____GGCACUAUGG______UUCAAUGCCGGUCA___CCGGCUUAUCACCUGAACCACACAUGAUAUUUGCCACUGGGCGAUGGGUGG
.............((((.(((((..........((((..................(((((......))))).(((((..((.....))..)))))..))))..)))))..))))... (-21.94 = -22.33 +   0.39)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,253,353 – 19,253,467
Length 114
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 78.05
Mean single sequence MFE -33.37
Consensus MFE -23.29
Energy contribution -23.85
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.70
SVM decision value 0.97
SVM RNA-class probability 0.893109
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19253353 114 - 23771897
CCACCCAUCGCCCAGUGGCAAAUAUCAUGUGUGGUUCAGGUGAUAAGCCGG---UGACCGGCAUUGAAUCCUAGGCAUAGUGCCUAGUAGUCGGUGGGCCUGGAAACAUCCAAUCGA
....(((..(((((.((((...((((((.((.....)).)))))).(((((---...)))))........((((((.....))))))..)))).))))).))).............. ( -44.10)
>DroPse_CAF1 25527 94 - 1
GAACUCAUCGCCCACUCGCAAAUAUCAUGUGUAGUUCAGGUGAUAAGCCGG---CGACCGGCA---------------AAUGCU----AAU-AGUAGGCCUAGAAACAUCUAAUCGA
((.......(((.(((.(((..((((((.((.....)).)))))).(((((---...))))).---------------..))).----...-))).))).((((....)))).)).. ( -25.40)
>DroSim_CAF1 88094 112 - 1
CCAACCAUCGCCCAGUGGCAAAUAUCAUGUGUGGUUCAGGUGAUAAGCCGGUGGUGACCGGCAUUGAAG-----CCAUAGUGCCCAGUAGUCGGUGGGCCUGGNNNNNNNNNNNNNN
....(((..((((.(((((...((((((.((.....)).)))))).((((((....))))))......)-----))))...(((........))))))).))).............. ( -38.70)
>DroEre_CAF1 85970 105 - 1
CCACCCAUCGCCCAGUGGCAAAUAUCAUGUGUGGUGCAGGUGAUAAGCCGG---UGACCGGCAUUGAAA-----CCAUAGUGCC----AGUCGGUAGGCCUGGAAACAUCUAAUCGA
.((((((((((...((((......))))..))))))..))))....(((..---((((.(((((((...-----...)))))))----.))))...))).((....))......... ( -32.60)
>DroYak_CAF1 112405 105 - 1
CCACCCAUCGCCCAGUGGCAAAUAUCAUGUGUGGUUCAGGUGAUAAGCCGG---UGACCGGCAUUGAAA-----CCACAGUGCC----AGUCGGUAGGCCUGGAAACAUCUAAUCGA
....(((..(((....(((...((((((.((.....)).)))))).)))(.---((((.(((((((...-----...)))))))----.)))).).))).))).............. ( -34.00)
>DroPer_CAF1 25464 94 - 1
GAACUCAUCGCCCACUCGCAAAUAUCAUGUGUAGUUCAGGUGAUAAGCCGG---CGACCGGCA---------------AAUGCU----AAU-AGUAGGCCUAGAAACAUCUAAUCGA
((.......(((.(((.(((..((((((.((.....)).)))))).(((((---...))))).---------------..))).----...-))).))).((((....)))).)).. ( -25.40)
>consensus
CCACCCAUCGCCCAGUGGCAAAUAUCAUGUGUGGUUCAGGUGAUAAGCCGG___UGACCGGCAUUGAA______CCAUAGUGCC____AGUCGGUAGGCCUGGAAACAUCUAAUCGA
....(((..(((.(.((((...((((((.((.....)).)))))).(((((......)))))...........................)))).).))).))).............. (-23.29 = -23.85 +   0.56)

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 12:40:12 2006