Locus 6430

Sequence ID 2L_DroMel_CAF1
Location 18,080,222 – 18,080,420
Length 198
Max. P 0.995020
window10259 window10260 window10261 window10262 window10263

overview

Window 9

Location 18,080,222 – 18,080,342
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -45.18
Consensus MFE -39.26
Energy contribution -40.08
Covariance contribution 0.81
Combinations/Pair 1.13
Mean z-score -1.97
Structure conservation index 0.87
SVM decision value 0.99
SVM RNA-class probability 0.896095
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18080222 120 + 22407834
CCAGCAAAAGAUCUGGGUCUUCUCCAUGGGAGGCCUGAUCCUGGCAAUUGGGAUUUUUCUGGCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGAAGUCUUUUGCCCCUGGCUCC
((((((((((((..(((((((((....)))))))))(((((..((....(((((....((((((.......))))))....))))).))...)))))....)))))))))...))).... ( -46.40)
>DroSec_CAF1 287438 120 + 1
CCAGCAAAAGAUCUGGGUCUUCUCCAUGGGAGGCCUGAUCCUGGCCAUUGGAAUUUUUCUGUCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCC
((((((((((((..(((((((((....)))))))))(((((((((((..((.......(((....)))))))))))((((.....))))...)))))....)))))))))...))).... ( -44.21)
>DroSim_CAF1 289482 120 + 1
CCAGCAAAAGAUCUGGGUUUUCUCCAUGGGAGGCCUGAUCCUGGCCAUUGGAAUUUUUCUGGCCUCUGCCUGGCCAGCCGUGUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCC
((((((((((((..(((((((((....)))))))))(((((((((((..(((.....)))(((....)))))))))((((.....))))...)))))....)))))))))...))).... ( -44.50)
>DroYak_CAF1 304827 120 + 1
CCAGCAAAAGAUCUGGGUAUUCUCCAUGGGGGGCCUGAUCCUGGCGGUUGGGAUUUUUCUGGCCGCAGCCUGGCCCGCGGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCUUUGGCUCC
(((((((((((.(((.(.....(((((...(((((.....(((.((((..(((...)))..)))))))...)))))((.(.....).)).)))))..).)))))))))))...))).... ( -45.60)
>consensus
CCAGCAAAAGAUCUGGGUCUUCUCCAUGGGAGGCCUGAUCCUGGCCAUUGGAAUUUUUCUGGCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCC
.........((((.(((((((((....)))))))))))))..(((((..(((((....((((((.......))))))....)))))(((((.((((.....)))).)))))..))))).. (-39.26 = -40.08 +   0.81)

alignment

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secondary structure

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Window 0

Location 18,080,262 – 18,080,381
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.07
Mean single sequence MFE -39.45
Consensus MFE -29.02
Energy contribution -29.90
Covariance contribution 0.88
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.74
SVM decision value 0.24
SVM RNA-class probability 0.649068
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18080262 119 + 22407834
CUGGCAAUUGGGAUUUUUCUGGCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGAAGUCUUUUGCCCCUGGCUCCCAACUCUUUUAUCUACAAUCGCUGGGUGACUACG-CCCAC
..(((..((((((......(((((.......)))))((((......(((((.((((.....)))).)))))..)))))))))).................(.(((....)))))-))... ( -38.10)
>DroSec_CAF1 287478 119 + 1
CUGGCCAUUGGAAUUUUUCUGUCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUUUACAAUCGCUGGGUGACCACG-CCCAU
..(((.((((........(((....)))...((((((..(.....)(((((.((((.....)))).))))).)))))).................)))).)))(((((....))-))).. ( -33.40)
>DroSim_CAF1 289522 120 + 1
CUGGCCAUUGGAAUUUUUCUGGCCUCUGCCUGGCCAGCCGUGUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUCUACAAUCGCUGGGGGACUACGGCCCAG
..((((....((((((...(((((.......)))))((((.....))))...))))))((((((....(((...)))(((((.(................).)))))))))))))))... ( -44.29)
>DroYak_CAF1 304867 119 + 1
CUGGCGGUUGGGAUUUUUCUGGCCGCAGCCUGGCCCGCGGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCUUUGGCUCCCAACUCCUUUAUCUACAAUCGCUGGGUGACCACG-CCCAU
..(((((((((((........(((((.((...))..))))).....(((((.((((.....)))).)))))......)))))))..................(((....)))))-))... ( -42.00)
>consensus
CUGGCCAUUGGAAUUUUUCUGGCCUCAGCCUGGCCAGCCGUAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUCUACAAUCGCUGGGUGACCACG_CCCAU
..(((((..(((((....((((((.......))))))....)))))(((((.((((.....)))).)))))..)))))........................((((.........)))). (-29.02 = -29.90 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,080,262 – 18,080,381
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.07
Mean single sequence MFE -42.50
Consensus MFE -36.16
Energy contribution -36.23
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.13
Structure conservation index 0.85
SVM decision value 1.25
SVM RNA-class probability 0.936304
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18080262 119 - 22407834
GUGGG-CGUAGUCACCCAGCGAUUGUAGAUAAAAGAGUUGGGAGCCAGGGGCAAAAGACUUCGAAUCCAUUGCCGAGAUACGGCUGGCCAGGCUGAGGCCAGAAAAAUCCCAAUUGCCAG
.((((-((.((((.((((((..((........))..)))))).(((...)))....)))).))........((((.....))))(((((.......))))).......))))........ ( -38.40)
>DroSec_CAF1 287478 119 - 1
AUGGG-CGUGGUCACCCAGCGAUUGUAAAUAAAGGAGUUGGGGGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGAUACGGCUGGCCAGGCUGAGGACAGAAAAAUUCCAAUGGCCAG
((((.-(((((((.((((((..((........))..)))))).(((...)))....)))))))...)))).((((.....))))((((((...((.(((........))))).)))))). ( -43.30)
>DroSim_CAF1 289522 120 - 1
CUGGGCCGUAGUCCCCCAGCGAUUGUAGAUAAAGGAGUUGGGGGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGACACGGCUGGCCAGGCAGAGGCCAGAAAAAUUCCAAUGGCCAG
((((..((((((((((((((..((........))..)))))))(((...)))....)))))))...(((((((((.....)))((((((.......))))))........)))))))))) ( -49.80)
>DroYak_CAF1 304867 119 - 1
AUGGG-CGUGGUCACCCAGCGAUUGUAGAUAAAGGAGUUGGGAGCCAAAGGCAAAAGACUACGAAUCCAUUGCCGAGAUACCGCGGGCCAGGCUGCGGCCAGAAAAAUCCCAACCGCCAG
.((((-(((((((.((((((..((........))..)))))).(((...)))....))))))).................((((((......))))))..........))))........ ( -38.50)
>consensus
AUGGG_CGUAGUCACCCAGCGAUUGUAGAUAAAGGAGUUGGGAGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGAUACGGCUGGCCAGGCUGAGGCCAGAAAAAUCCCAAUGGCCAG
.((((.(((((((.((((((..((........))..)))))).(((...)))....)))))))........((((.....)))).((((.......))))........))))........ (-36.16 = -36.23 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,080,302 – 18,080,420
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.72
Mean single sequence MFE -31.31
Consensus MFE -25.60
Energy contribution -26.91
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -1.82
Structure conservation index 0.82
SVM decision value 0.44
SVM RNA-class probability 0.735432
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18080302 118 + 22407834
UAUCUCGGCAAUGGAUUCGAAGUCUUUUGCCCCUGGCUCCCAACUCUUUUAUCUACAAUCGCUGGGUGACUACG-CCCACGCCGGUAUAU-AGCACAGUUUUCCUCUUCAACUGGACUAA
(((..((((..(((((..((((......(((...)))........)))).))))).....(.((((((....))-)))))))))..)))(-((..(((((.........)))))..))). ( -29.74)
>DroSec_CAF1 287518 118 + 1
UAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUUUACAAUCGCUGGGUGACCACG-CCCAUGCCGGUAUAU-AGCACAGUUUUCCUCUUCAACUGGACUAA
(((..(((((.(((....(.(((.....(((...))).....))).).............(((((....))).)-)))))))))..)))(-((..(((((.........)))))..))). ( -29.40)
>DroSim_CAF1 289562 120 + 1
UGUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUCUACAAUCGCUGGGGGACUACGGCCCAGGCCGGUAUAUGAGCACAGUUUUCCUUUUCAAAUGGACUAA
(((((((((((.((((.....)))).)))))..(((((((((.(................).)))))).)))((((....))))......))).)))....(((.........))).... ( -35.49)
>DroYak_CAF1 304907 118 + 1
UAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCUUUGGCUCCCAACUCCUUUAUCUACAAUCGCUGGGUGACCACG-CCCAUGCCGCUAUAU-AGCACAGUUUUCCUCUUUAACUGGACUAA
(((..(((((.(((....((((..........((((...)))).........))))....(((((....))).)-)))))))))..)))(-((..(((((.........)))))..))). ( -30.61)
>consensus
UAUCUCGGCAAUGGAUUCGUAGUCUUUUGCCCCUGGCCCCCAACUCCUUUAUCUACAAUCGCUGGGUGACCACG_CCCAUGCCGGUAUAU_AGCACAGUUUUCCUCUUCAACUGGACUAA
(((..(((((.(((...(((((((....(((...))).((((.(................).)))).)))))))..))))))))..)))..((..(((((.........)))))..)).. (-25.60 = -26.91 +   1.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,080,302 – 18,080,420
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.72
Mean single sequence MFE -41.92
Consensus MFE -38.19
Energy contribution -38.38
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -3.39
Structure conservation index 0.91
SVM decision value 2.53
SVM RNA-class probability 0.995020
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18080302 118 - 22407834
UUAGUCCAGUUGAAGAGGAAAACUGUGCU-AUAUACCGGCGUGGG-CGUAGUCACCCAGCGAUUGUAGAUAAAAGAGUUGGGAGCCAGGGGCAAAAGACUUCGAAUCCAUUGCCGAGAUA
.(((..(((((.........)))))..))-).....((((((((.-((.((((.((((((..((........))..)))))).(((...)))....)))).))...))).)))))..... ( -39.70)
>DroSec_CAF1 287518 118 - 1
UUAGUCCAGUUGAAGAGGAAAACUGUGCU-AUAUACCGGCAUGGG-CGUGGUCACCCAGCGAUUGUAAAUAAAGGAGUUGGGGGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGAUA
.(((..(((((.........)))))..))-).....((((((((.-(((((((.((((((..((........))..)))))).(((...)))....)))))))...))).)))))..... ( -44.10)
>DroSim_CAF1 289562 120 - 1
UUAGUCCAUUUGAAAAGGAAAACUGUGCUCAUAUACCGGCCUGGGCCGUAGUCCCCCAGCGAUUGUAGAUAAAGGAGUUGGGGGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGACA
...(((....(((..((.....))....))).....((((.((((.((((((((((((((..((........))..)))))))(((...)))....)))))))..))))..)))).))). ( -39.60)
>DroYak_CAF1 304907 118 - 1
UUAGUCCAGUUAAAGAGGAAAACUGUGCU-AUAUAGCGGCAUGGG-CGUGGUCACCCAGCGAUUGUAGAUAAAGGAGUUGGGAGCCAAAGGCAAAAGACUACGAAUCCAUUGCCGAGAUA
.(((..(((((.........)))))..))-)(((..((((((((.-(((((((.((((((..((........))..)))))).(((...)))....)))))))...))).)))))..))) ( -44.30)
>consensus
UUAGUCCAGUUGAAGAGGAAAACUGUGCU_AUAUACCGGCAUGGG_CGUAGUCACCCAGCGAUUGUAGAUAAAGGAGUUGGGAGCCAGGGGCAAAAGACUACGAAUCCAUUGCCGAGAUA
..((..(((((.........)))))..)).......((((((((..(((((((.((((((..((........))..)))))).(((...)))....)))))))...))).)))))..... (-38.19 = -38.38 +   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 12:10:54 2006