Locus 8554

Sequence ID X_DroMel_CAF1
Location 21,180,690 – 21,180,881
Length 191
Max. P 0.947933
window14074 window14075 window14076

overview

Window 4

Location 21,180,690 – 21,180,810
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.67
Mean single sequence MFE -39.98
Consensus MFE -33.12
Energy contribution -33.50
Covariance contribution 0.38
Combinations/Pair 1.12
Mean z-score -2.44
Structure conservation index 0.83
SVM decision value 1.38
SVM RNA-class probability 0.947933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21180690 120 + 22224390
AAGAAGCCUUGAGGGAUAUUCUCCGGCAGCGGCAUCUUACGUUUCGGGCUUGUCCAGGGACUUUUUGAUAUCCAGAGAACUUUCCCAAAGAUCAGGAGAAUUCCUGACAGCUGCUGCAAA
.((((.((.....))...))))...((((((((.((((.......(((....))).((((.((((((.....))))))....)))).))))(((((......)))))..))))))))... ( -39.80)
>DroSec_CAF1 6879 120 + 1
AAAAAGCCUUGUGGGAUAUUCUCCGGCAGCGGCAUCUUACGUAUCAGGCUUGUCCAGGGACAUUUUGAUAUCCAGAGAACUUUCCCAAAGAUCAGGAGACUUCCUGACAGCUGCUGCAAA
.............(((.....))).((((((((.((((..((((((((..((((....)))).))))))))...)))).............(((((......)))))..))))))))... ( -39.20)
>DroEre_CAF1 7006 120 + 1
AGGAAGCCUUGUGGGAUUUUCUCCGGCAACGGCAUCCUAUGUUUCAGGCUUGUCCAGGGAUUUCUUGAUAUCCAGAGAACUUUCCCAAAGAUCGGGAGAUUUCCUGACAGCUGCUGCAAA
((((.(((((((.(((.....))).)))).))).)))).(((....((((.(((.((((((((((.(....).)))))..((((((.......)))))).))))))))))))...))).. ( -43.50)
>DroYak_CAF1 215 120 + 1
AGGAAGCCUUGUGGGAUUUUCUCCGGCAACAGCAUCCUAUGUUUCAGGCUUGUCCAGGGAUUUCUUGAUAUCCAGAGAACUAUCCCAAAGAUCAGGAGAUUUUCUGACAGCUGCUGCAAA
((((.((.((((.(((.....))).))))..)).)))).(((....((((.(((..(((((((((((((.....((......))......)))))))))))))..)))))))...))).. ( -37.40)
>consensus
AAGAAGCCUUGUGGGAUAUUCUCCGGCAACGGCAUCCUACGUUUCAGGCUUGUCCAGGGACUUCUUGAUAUCCAGAGAACUUUCCCAAAGAUCAGGAGAUUUCCUGACAGCUGCUGCAAA
((((.(((((((.(((.....))).)))).))).))))..((....((((.(((.((((((((((((((.....(((....)))......))))))))).))))))))))))...))... (-33.12 = -33.50 +   0.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,180,690 – 21,180,810
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.67
Mean single sequence MFE -35.88
Consensus MFE -30.69
Energy contribution -30.75
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -1.56
Structure conservation index 0.86
SVM decision value 0.31
SVM RNA-class probability 0.683003
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21180690 120 - 22224390
UUUGCAGCAGCUGUCAGGAAUUCUCCUGAUCUUUGGGAAAGUUCUCUGGAUAUCAAAAAGUCCCUGGACAAGCCCGAAACGUAAGAUGCCGCUGCCGGAGAAUAUCCCUCAAGGCUUCUU
...(((((.((.(((((((....))))))).((((((...((((...((((........))))..))))...)))))).........)).))))).(((.....)))............. ( -37.20)
>DroSec_CAF1 6879 120 - 1
UUUGCAGCAGCUGUCAGGAAGUCUCCUGAUCUUUGGGAAAGUUCUCUGGAUAUCAAAAUGUCCCUGGACAAGCCUGAUACGUAAGAUGCCGCUGCCGGAGAAUAUCCCACAAGGCUUUUU
.....(((....(((((((....)))))))((((((((..(((((((((.(((((...((((....))))....)))))(....).........))))))))).))))).)))))).... ( -39.60)
>DroEre_CAF1 7006 120 - 1
UUUGCAGCAGCUGUCAGGAAAUCUCCCGAUCUUUGGGAAAGUUCUCUGGAUAUCAAGAAAUCCCUGGACAAGCCUGAAACAUAGGAUGCCGUUGCCGGAGAAAAUCCCACAAGGCUUCCU
...((....))..(((((.....((((((...))))))..((((...((((........))))..))))...))))).....((((.(((.(((..(((.....)))..)))))).)))) ( -34.80)
>DroYak_CAF1 215 120 - 1
UUUGCAGCAGCUGUCAGAAAAUCUCCUGAUCUUUGGGAUAGUUCUCUGGAUAUCAAGAAAUCCCUGGACAAGCCUGAAACAUAGGAUGCUGUUGCCGGAGAAAAUCCCACAAGGCUUCCU
...((((((((.(((((........))))).((..((...((((...((((........))))..))))...))..)).........)))))))).(((.....)))............. ( -31.90)
>consensus
UUUGCAGCAGCUGUCAGGAAAUCUCCUGAUCUUUGGGAAAGUUCUCUGGAUAUCAAAAAAUCCCUGGACAAGCCUGAAACAUAAGAUGCCGCUGCCGGAGAAAAUCCCACAAGGCUUCCU
...(((((.((.(((((((....))))))).((((((...((((...((((........))))..))))...)))))).........)).))))).(((.....)))............. (-30.69 = -30.75 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,180,770 – 21,180,881
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 93.09
Mean single sequence MFE -32.03
Consensus MFE -28.46
Energy contribution -28.27
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -1.61
Structure conservation index 0.89
SVM decision value 0.47
SVM RNA-class probability 0.749210
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21180770 111 + 22224390
UUUCCCAAAGAUCAGGAGAAUUCCUGACAGCUGCUGCAAAGAUGGUAUCCCAAAUGGGAGCAAGCGAACUCCGCUGGCUCCCCAUAUCCAGGACCAAAGACAAACCAUCGA
...........(((((......)))))..((....))...((((((.(((.....((((((.((((.....)))).))))))........)))(....)....)))))).. ( -33.42)
>DroSec_CAF1 6959 111 + 1
UUUCCCAAAGAUCAGGAGACUUCCUGACAGCUGCUGCAAAGAUGGUAUCCCAAAUGGGAGCAAGCGAACUCCGCUGGUUGCCCAUACCCAGGACCAAAGACAAACCAUCGA
...........(((((......)))))..((....))...((((((.......((((((((.((((.....)))).))).))))).(....)...........)))))).. ( -31.10)
>DroEre_CAF1 7086 111 + 1
UUUCCCAAAGAUCGGGAGAUUUCCUGACAGCUGCUGCAAAAAUGGUAUCCCAAAUGGGAGCAGGCGAACUCCGCUGGAUGCCAAUGCCCAGGACCAAAGAUAAGCCAUCGA
((((((.......))))))..(((((...((....)).....((((((((....((....))((((.....)))))))))))).....))))).....(((.....))).. ( -32.10)
>DroYak_CAF1 295 111 + 1
UAUCCCAAAGAUCAGGAGAUUUUCUGACAGCUGCUGCAAAGAUGGUAUCCCAAAUGGGAGCAAGCGAACUCCGCUGGCUGCCCAUGCCCAGGACCAAAGAUAAGCCAUCGA
...........((((((....))))))..((....))...((((((.(((...((((((((.((((.....)))).))).))))).....)))(....)....)))))).. ( -31.50)
>consensus
UUUCCCAAAGAUCAGGAGAUUUCCUGACAGCUGCUGCAAAGAUGGUAUCCCAAAUGGGAGCAAGCGAACUCCGCUGGCUGCCCAUACCCAGGACCAAAGACAAACCAUCGA
...........((((((....))))))..((....))...((((((.(((...((((((((.((((.....)))).))).))))).....)))(....)....)))))).. (-28.46 = -28.27 +  -0.19)

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 13:07:10 2006