Locus 832

Sequence ID 3L_DroMel_CAF1
Location 2,532,166 – 2,532,313
Length 147
Max. P 0.664879
window1278 window1279 window1280

overview

Window 8

Location 2,532,166 – 2,532,275
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Mean single sequence MFE -33.46
Consensus MFE -24.20
Energy contribution -25.70
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.40
Structure conservation index 0.72
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2532166 109 + 23771897
U-G----------GAAAUAUAUACAAAUUUCUCCCCCUGUACGGAUAGAUGGAUUGCUGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCA
.-.----------(((((........)))))(((..((((....))))..))).(((((((......(((((((((......))))))))))))))))(((((...........))))). ( -33.30)
>DroSec_CAF1 155026 120 + 1
CUGGGAAUUUAAAAAGAUAUAUAGAAAUUUCUCCCCCUGUACGGAUAGAUGGAUUGCUGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCA
...(((((((..............)))))))(((..((((....))))..))).(((((((......(((((((((......))))))))))))))))(((((...........))))). ( -33.44)
>DroSim_CAF1 152594 120 + 1
AUGCGAAUUUAAAAAGAUAUAUAGAAAUUUCUCCCCCUGUACGGAUAGAUGGAUUGCAGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCA
.(((........................((((((..(((((.............)))))..)))))).((((((((......)))))))).....)))(((((...........))))). ( -32.72)
>DroYak_CAF1 155242 120 + 1
AUGGAAAUUUGUCCAGAUAUAUAUAAAUUUCGCGCACUGUACGUAUAUAUGGAUUGCAGAUGGGGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCA
.((((......))))..............((((((.((((..((...((((((((((((.(.((.........)).)..)))))))))))).)).))))))))))............... ( -34.40)
>consensus
AUGGGAAUUUAAAAAGAUAUAUAGAAAUUUCUCCCCCUGUACGGAUAGAUGGAUUGCAGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCA
...............................(((..((((....))))..))).(((((((......(((((((((......))))))))))))))))(((((...........))))). (-24.20 = -25.70 +   1.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,532,195 – 2,532,313
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 94.63
Mean single sequence MFE -34.22
Consensus MFE -28.08
Energy contribution -28.83
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.82
SVM decision value 0.28
SVM RNA-class probability 0.664879
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2532195 118 + 23771897
ACGGAUAGAUGGAUUGCUGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCACAGGACGGUGGAGACAGAGCCAAGAAAGAAAGGCUGAA
.((...........(((((((......(((((((((......))))))))))))))))(((((...........)))))......)).((....)).((((..........))))... ( -35.80)
>DroSec_CAF1 155066 118 + 1
ACGGAUAGAUGGAUUGCUGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCACAGGACGGCGGAGACAAAGCCAAGAAAGAAAGGCAGAA
.((...........(((((((......(((((((((......))))))))))))))))(((((...........)))))......))..(....)...(((..........))).... ( -34.40)
>DroSim_CAF1 152634 118 + 1
ACGGAUAGAUGGAUUGCAGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCACAGGACGGCCGAGACAAAGCCAAGAAAGAAAGGCAGAA
.(((.....((..(((..((((.....(((((((((......)))))))))..)))).(((((...........))))).)))..)).))).......(((..........))).... ( -33.40)
>DroYak_CAF1 155282 118 + 1
ACGUAUAUAUGGAUUGCAGAUGGGGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCAAAGGACGGUGGAGACAAAGCCAAGCGAGAAAGGCAGAA
..((...((((((((((((.(.((.........)).)..)))))))))))).)).((.(((((...........)))))...((.(..((....))..)))..))............. ( -33.30)
>consensus
ACGGAUAGAUGGAUUGCAGCUGGAGAAUGCAGACUGAGACUGCAGUCUGUGGGCAGCAGGCGUGACAACUACAAAUGCCACAGGACGGCGGAGACAAAGCCAAGAAAGAAAGGCAGAA
.((...........(((((((......(((((((((......))))))))))))))))(((((...........)))))......))...........(((..........))).... (-28.08 = -28.83 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,532,195 – 2,532,313
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 94.63
Mean single sequence MFE -27.90
Consensus MFE -23.15
Energy contribution -24.40
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.83
SVM decision value -0.03
SVM RNA-class probability 0.519376
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2532195 118 - 23771897
UUCAGCCUUUCUUUCUUGGCUCUGUCUCCACCGUCCUGUGGCAUUUGUAGUUGUCACGCCUGCUGCCCACAGACUGCAGUCUCAGUCUGCAUUCUCCAGCAGCAAUCCAUCUAUCCGU
...((((..........))))................((((((........))))))...((((((....(((.(((((.......))))).)))...)))))).............. ( -30.00)
>DroSec_CAF1 155066 118 - 1
UUCUGCCUUUCUUUCUUGGCUUUGUCUCCGCCGUCCUGUGGCAUUUGUAGUUGUCACGCCUGCUGCCCACAGACUGCAGUCUCAGUCUGCAUUCUCCAGCAGCAAUCCAUCUAUCCGU
....((...........(((.........))).....((((((........)))))))).((((((....(((.(((((.......))))).)))...)))))).............. ( -29.90)
>DroSim_CAF1 152634 118 - 1
UUCUGCCUUUCUUUCUUGGCUUUGUCUCGGCCGUCCUGUGGCAUUUGUAGUUGUCACGCCUGCUGCCCACAGACUGCAGUCUCAGUCUGCAUUCUCCAGCUGCAAUCCAUCUAUCCGU
...((((...(.....(((((.......)))))....).)))).(((((((((....((.....))...(((((((......))))))).......)))))))))............. ( -29.00)
>DroYak_CAF1 155282 118 - 1
UUCUGCCUUUCUCGCUUGGCUUUGUCUCCACCGUCCUUUGGCAUUUGUAGUUGUCACGCCUGCUGCCCACAGACUGCAGUCUCAGUCUGCAUUCCCCAUCUGCAAUCCAUAUAUACGU
....(((..........)))...........(((....(((...((((((.((....((.....))...(((((((......))))))).......)).)))))).))).....))). ( -22.70)
>consensus
UUCUGCCUUUCUUUCUUGGCUUUGUCUCCACCGUCCUGUGGCAUUUGUAGUUGUCACGCCUGCUGCCCACAGACUGCAGUCUCAGUCUGCAUUCUCCAGCAGCAAUCCAUCUAUCCGU
....(((..........))).................((((((........))))))...((((((....(((.(((((.......))))).)))...)))))).............. (-23.15 = -24.40 +   1.25)

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 09:52:17 2006