Locus 8375

Sequence ID X_DroMel_CAF1
Location 20,797,225 – 20,797,365
Length 140
Max. P 0.997349
window13754 window13755 window13756

overview

Window 4

Location 20,797,225 – 20,797,338
Length 113
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 91.75
Mean single sequence MFE -51.10
Consensus MFE -40.70
Energy contribution -41.30
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -3.32
Structure conservation index 0.80
SVM decision value 2.84
SVM RNA-class probability 0.997349
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20797225 113 - 22224390
UG------CAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
.(------((.((((((((((....((.......)).)))))))))))))((((...(((((...((((((....))).)))....))).))((((....))))))))........... ( -49.00)
>DroSec_CAF1 125711 111 - 1
--------UAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCACCUAAUGAGGAUGGGCGGCCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
--------..(((((.((((((((....)))))))).))))).(((((((.((....(((((((.((((((....))).)))..))))).))((((....)))))))))......)))) ( -49.60)
>DroSim_CAF1 62754 119 - 1
UGCAGCAGCAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
.(((.((((.(((((.((((((((....)))))))).))))).)))))))((((...(((((...((((((....))).)))....))).))((((....))))))))........... ( -54.90)
>DroEre_CAF1 48424 119 - 1
UGCAGCAGCAGCAGCUGCAGUUGUUGCUGCGAUUGUAGUUGCAGCUGUGCGCCUAAUGAGGAGGGGCGACCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
.(((.((((.((((((((((((((....)))))))))))))).)))))))((((...(((((.((....)).(((........)))))).))((((....))))))))........... ( -53.70)
>DroYak_CAF1 100655 110 - 1
UGCA---------GCUGCAGUUGUUGCUGCGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGUAGGGGCGGCCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
((((---------((.((((((((....)))))))).))))))(((((((.((((.....)))).)))(((((((........))))....(((((....)))))))).......)))) ( -48.30)
>consensus
UGCA____CAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCACGUAGCAUCCAUCGGUGGCAACAUCGGGCAAAUAAUCAGC
..........(((((.((((((((....)))))))).))))).((((..(((((.........)))))(((((((........))))....(((((....)))))))).......)))) (-40.70 = -41.30 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,797,264 – 20,797,365
Length 101
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 82.48
Mean single sequence MFE -34.70
Consensus MFE -25.07
Energy contribution -26.11
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -2.35
Structure conservation index 0.72
SVM decision value 1.41
SVM RNA-class probability 0.950833
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20797264 101 + 22224390
GUGCCGCAUGGCCGCCCCUCCUCAUUAGGCGCACAGCUGCAGCAACAAUCGUAGCAACAACUGCAGCUGCUG------CAACUCCAUGUGCAACAUACAAAACGCAG---------
.(((.((((((..(((...........)))((((((((((((..................))))))))).))------)....)))))))))...............--------- ( -32.97)
>DroSec_CAF1 125750 95 + 1
GUGCCGCAUGGCCGCCCAUCCUCAUUAGGUGCACAGCUGCAGCAACAAUCGUAGCAACAACUGCAGCUGCUA------------CAUCUGCAACAUGCAAAGCGCAG---------
((((.(((((...((...........(((((..(((((((((..................)))))))))...------------)))))))..)))))...))))..--------- ( -29.87)
>DroSim_CAF1 62793 107 + 1
GUGCCGCAUGGCCGCCCCUCCUCAUUAGGCGCACAGCUGCAGCAACAAUCGUAGCAACAACUGCAGCUGCUGCUGCUGCAACUCCAUCUGCAACAUGCAAAGCGCAG---------
((((.((((((((..............)))(((((((.(((((.((....)).(((.....))).))))).)))).)))..............)))))...))))..--------- ( -38.24)
>DroEre_CAF1 48463 116 + 1
GUGCCGCAUGGUCGCCCCUCCUCAUUAGGCGCACAGCUGCAACUACAAUCGCAGCAACAACUGCAGCUGCUGCUGCUGCAACUCCAUCUGCAACAUGCAAAGCGCUGCACCUACUG
(((((....((........))......)))))...(((((..........)))))......((((((.(((((((.((((........)))).)).))..)))))))))....... ( -36.90)
>DroYak_CAF1 100694 107 + 1
GUGCCGCAUGGCCGCCCCUACUCAUUAGGCGCACAGCUGCAGCAACAAUCGCAGCAACAACUGCAGC---------UGCAACUCCAUUUGCAACAUGCAGAGGGCAGCAUCUGCUG
..((.((.((..((((...........))))..)))).))((((......((((......)))).((---------(((....((.(((((.....))))))))))))...)))). ( -35.50)
>consensus
GUGCCGCAUGGCCGCCCCUCCUCAUUAGGCGCACAGCUGCAGCAACAAUCGUAGCAACAACUGCAGCUGCUG____UGCAACUCCAUCUGCAACAUGCAAAGCGCAG_________
((((.((((((.((((...........))))).(((((((((..................)))))))))........................)))))...))))........... (-25.07 = -26.11 +   1.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,797,264 – 20,797,365
Length 101
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 82.48
Mean single sequence MFE -46.28
Consensus MFE -32.10
Energy contribution -32.78
Covariance contribution 0.68
Combinations/Pair 1.07
Mean z-score -2.84
Structure conservation index 0.69
SVM decision value 2.05
SVM RNA-class probability 0.986567
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20797264 101 - 22224390
---------CUGCGUUUUGUAUGUUGCACAUGGAGUUG------CAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCAC
---------............(((((((..((((((((------(((((...((((((((....)))))))))))))))))).(((.(((.......))).))).)))))))))). ( -41.20)
>DroSec_CAF1 125750 95 - 1
---------CUGCGCUUUGCAUGUUGCAGAUG------------UAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCACCUAAUGAGGAUGGGCGGCCAUGCGGCAC
---------.(((.....)))(((((((....------------..(((((.((((((((....)))))))).))))).(((((.(((((....))).)).)))))..))))))). ( -40.30)
>DroSim_CAF1 62793 107 - 1
---------CUGCGCUUUGCAUGUUGCAGAUGGAGUUGCAGCAGCAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCAC
---------(((((...(((.((((((((......)))))))))))(((((.((((((((....)))))))).))))).(((((.(.(((....)))..).)))))..)))))... ( -46.10)
>DroEre_CAF1 48463 116 - 1
CAGUAGGUGCAGCGCUUUGCAUGUUGCAGAUGGAGUUGCAGCAGCAGCAGCUGCAGUUGUUGCUGCGAUUGUAGUUGCAGCUGUGCGCCUAAUGAGGAGGGGCGACCAUGCGGCAC
.....(.((((.(((((((((((((((((.((.(((((((((((((((.......))))))))))))))).)).))))))).)))).(((....))).))))))....)))).).. ( -53.40)
>DroYak_CAF1 100694 107 - 1
CAGCAGAUGCUGCCCUCUGCAUGUUGCAAAUGGAGUUGCA---------GCUGCAGUUGUUGCUGCGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGUAGGGGCGGCCAUGCGGCAC
..(((((........))))).(((((((..((((((((((---------((.((((((((....)))))))).))))))))).(((.((((.....)))).))).)))))))))). ( -50.40)
>consensus
_________CUGCGCUUUGCAUGUUGCAGAUGGAGUUGCA____CAGCAGCUGCAGUUGUUGCUACGAUUGUUGCUGCAGCUGUGCGCCUAAUGAGGAGGGGCGGCCAUGCGGCAC
...........((.....)).(((((((..(((.............(((((((((((....((.......)).))))))))))).(((((.........))))).)))))))))). (-32.10 = -32.78 +   0.68)

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 13:02:25 2006