Locus 1495

Sequence ID 2R_DroMel_CAF1
Location 5,670,711 – 5,670,836
Length 125
Max. P 0.982975
window2536 window2537 window2538

overview

Window 6

Location 5,670,711 – 5,670,801
Length 90
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 72.04
Mean single sequence MFE -20.11
Consensus MFE -13.52
Energy contribution -13.28
Covariance contribution -0.25
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.67
SVM decision value 1.04
SVM RNA-class probability 0.904450
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5670711 90 + 20766785
CAAAAAAAAAAAGAAACCCUGAGGCGUUCUUCUCACGGCCCCCUAUUACUAGGGUUGAAACAGCCAGCAAAC----AUAU----AUCAA-----UGUGAUUAU
................((.(((((......))))).))..(((((....))))).................(----((((----....)-----))))..... ( -13.70)
>DroSec_CAF1 8129 84 + 1
-----AAAAAAGGAUACCCUGGGGCGUUCUUCUCACGGCCCCCUAUUACUAGGGUG-----UGCCGGCAUAC----AUAUGUAUAGGAA-----UGUGAUUAU
-----.....(((....)))...((((((((....((((((((((....))))).)-----.))))..((((----....)))))))))-----)))...... ( -24.80)
>DroSim_CAF1 8143 82 + 1
-----A--AAAGGAUACCCUGGGGCGUUCUUCUCACGGCCCCCUAUUACUAGGGUG-----UGCCAGCAUAC----AUAUGUAUAGGAA-----UGUGAUUAU
-----.--.(((((..((....))..))))).(((((((((((((....))))).)-----.)))...((((----....)))).....-----.)))).... ( -24.50)
>DroYak_CAF1 8217 95 + 1
CA---AAAAAAAAAAACCCUGGGGCGUUCUACUCACGGCCCCCUACUACAAGGGUU-----UGUAGACGUAUUAAUACAUUUAAAAAAAUACAAUAAAAUCAU
..---........((((((((((((((.......)).)))))........))))))-----)......(((((..............)))))........... ( -17.44)
>consensus
_____AAAAAAAGAAACCCUGGGGCGUUCUUCUCACGGCCCCCUAUUACUAGGGUG_____UGCCAGCAUAC____AUAUGUAUAGGAA_____UGUGAUUAU
..............(((((((((((((.......)).)))))........))))))............................................... (-13.52 = -13.28 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,670,711 – 5,670,801
Length 90
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 72.04
Mean single sequence MFE -23.70
Consensus MFE -14.94
Energy contribution -14.75
Covariance contribution -0.19
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.63
SVM decision value 1.93
SVM RNA-class probability 0.982975
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5670711 90 - 20766785
AUAAUCACA-----UUGAU----AUAU----GUUUGCUGGCUGUUUCAACCCUAGUAAUAGGGGGCCGUGAGAAGAACGCCUCAGGGUUUCUUUUUUUUUUUG
....((((.-----((((.----(((.----(((....)))))).))))(((((....)))))....))))((((((.(((....)))))))))......... ( -22.90)
>DroSec_CAF1 8129 84 - 1
AUAAUCACA-----UUCCUAUACAUAU----GUAUGCCGGCA-----CACCCUAGUAAUAGGGGGCCGUGAGAAGAACGCCCCAGGGUAUCCUUUUUU-----
....((((.-----....(((((....----)))))..(((.-----..(((((....))))).)))))))((((.(..((....))..).))))...----- ( -26.80)
>DroSim_CAF1 8143 82 - 1
AUAAUCACA-----UUCCUAUACAUAU----GUAUGCUGGCA-----CACCCUAGUAAUAGGGGGCCGUGAGAAGAACGCCCCAGGGUAUCCUUU--U-----
....((((.-----....(((((....----)))))..(((.-----..(((((....))))).)))))))((((.(..((....))..).))))--.----- ( -26.50)
>DroYak_CAF1 8217 95 - 1
AUGAUUUUAUUGUAUUUUUUUAAAUGUAUUAAUACGUCUACA-----AACCCUUGUAGUAGGGGGCCGUGAGUAGAACGCCCCAGGGUUUUUUUUUUU---UG
...........(((((..(........)..)))))......(-----((((((........(((((.((.......))))))))))))))........---.. ( -18.60)
>consensus
AUAAUCACA_____UUCCUAUACAUAU____GUAUGCCGGCA_____AACCCUAGUAAUAGGGGGCCGUGAGAAGAACGCCCCAGGGUAUCCUUUUUU_____
................................................(((((........(((((.((.......))))))))))))............... (-14.94 = -14.75 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,670,746 – 5,670,836
Length 90
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 67.69
Mean single sequence MFE -17.95
Consensus MFE -8.27
Energy contribution -8.78
Covariance contribution 0.50
Combinations/Pair 1.11
Mean z-score -2.07
Structure conservation index 0.46
SVM decision value 0.95
SVM RNA-class probability 0.889143
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5670746 90 - 20766785
AACCAAAA---CAAAAGAAUUAUAUCAUAUAUAUUUCAAUAAUCACA-----UUGAU----AUAU----GUUUGCUGGCUGUUUCAACCCUAGUAAUAGGGGGCCG
........---..............((.((((((.(((((......)-----)))).----))))----)).))..((((.......(((((....))))))))). ( -19.31)
>DroSec_CAF1 8159 89 - 1
AACCAAAA---CAAAAGAGUUAUAUCAAAUAUAUUUCAAUAAUCACA-----UUCCUAUACAUAU----GUAUGCCGGCA-----CACCCUAGUAAUAGGGGGCCG
........---.....(((.(((((...))))).)))..........-----....(((((....----))))).((((.-----..(((((....))))).)))) ( -19.60)
>DroSim_CAF1 8171 89 - 1
AACCAAAA---CAAAAGAGUUAUAUCAAAUAUAUUUGAAUAAUCACA-----UUCCUAUACAUAU----GUAUGCUGGCA-----CACCCUAGUAAUAGGGGGCCG
........---.....((.((((.(((((....)))))))))))...-----....(((((....----)))))..(((.-----..(((((....))))).))). ( -19.80)
>DroYak_CAF1 8249 96 - 1
ACAAA-AAAAAUCAAAA-AUUGUU---UACAAAUUACGAUGAUUUUAUUGUAUUUUUUUAAAUGUAUUAAUACGUCUACA-----AACCCUUGUAGUAGGGGGCCG
.....-...........-.((((.---.(((((.(((((((....))))))).))).......(((....)))))..)))-----).((((......))))..... ( -13.10)
>consensus
AACCAAAA___CAAAAGAAUUAUAUCAAAUAUAUUUCAAUAAUCACA_____UUCCUAUACAUAU____GUAUGCCGGCA_____AACCCUAGUAAUAGGGGGCCG
...........................................................................((((........(((((....))))).)))) ( -8.27 =  -8.78 +   0.50)

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 10:06:12 2006