Locus 7946

Sequence ID 3L_DroMel_CAF1
Location 21,076,720 – 21,076,935
Length 215
Max. P 0.995563
window12959 window12960 window12961 window12962

overview

Window 9

Location 21,076,720 – 21,076,816
Length 96
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 88.03
Mean single sequence MFE -32.12
Consensus MFE -26.10
Energy contribution -26.35
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.68
Structure conservation index 0.81
SVM decision value 0.46
SVM RNA-class probability 0.746589
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21076720 96 - 23771897
CUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACGAUUGACUGGGUAACUCAGUCUGUGAACC--------------UGCUGAGAGUUCAUGGGA
(((.((((((..........(((((((...)))))))((((((((....))))).))).)))))))))((((((((((--------------(....)).))))))))). ( -31.00)
>DroSec_CAF1 131889 96 - 1
CUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACAAUUGACUGGGUAACUCAGUCUGUGAACC--------------UGAAGAGAGUUCAUGGGA
(((.((((((..........(((((((...)))))))...(((((........))))).)))))))))((((((((((--------------(....)).))))))))). ( -30.80)
>DroSim_CAF1 38169 96 - 1
CUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACAAUUGACUGGGUAACUCAGUCUGUGAACC--------------UGAAGAGAGUUCAUGGGA
(((.((((((..........(((((((...)))))))...(((((........))))).)))))))))((((((((((--------------(....)).))))))))). ( -30.80)
>DroEre_CAF1 54582 110 - 1
CUGCAGUUGCAUAAUUGAAGCGGCGAUUUAAUUGCUGCGGCAGUCUGGCGAUUGACUGGGUAACUCAGGCUGCGAACCGAGCUGAACUGAACUGAUGACAGUUCUUGGGA
.(((((((((...((((..((((((((...))))))))..))))...))).....(((((...)))))))))))..((((...((((((.........)))))))))).. ( -35.90)
>consensus
CUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACAAUUGACUGGGUAACUCAGUCUGUGAACC______________UGAAGAGAGUUCAUGGGA
(((.((((((..........(((((((...)))))))...(((((........))))).))))))))).((((((((.......................)))))))).. (-26.10 = -26.35 +   0.25)

alignment

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secondary structure

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Window 0

Location 21,076,738 – 21,076,856
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.64
Mean single sequence MFE -42.56
Consensus MFE -38.78
Energy contribution -38.78
Covariance contribution 0.00
Combinations/Pair 1.10
Mean z-score -1.90
Structure conservation index 0.91
SVM decision value 2.59
SVM RNA-class probability 0.995563
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21076738 118 - 23771897
ACGGGGGAAUCCCGUAUUCGUUUAUGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACGAUUGACUGGGUAACUCAGUCUGUGAACC--
.((..(((.(((((((......))))))).....((((((..(((((((...(((((......)))))))))))).)))))).)))..))...(((((((...)))))))........-- ( -41.10)
>DroSec_CAF1 131907 118 - 1
ACGGGGGAAUCCCGUAUUCGUUUAUGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACAAUUGACUGGGUAACUCAGUCUGUGAACC--
.((((.((((((((((......))).))))))).((((((..(((((((...(((((......)))))))))))).)))))).)))).((...(((((((...)))))))..))....-- ( -40.40)
>DroSim_CAF1 38187 118 - 1
ACGGGGGAAUCCCGUAUUCGUUUACGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACAAUUGACUGGGUAACUCAGUCUGUGAACC--
(((((.....)))))....(((((((.((((...((((((..(((((((...(((((......)))))))))))).)))))))))).......(((((((...)))))))))))))).-- ( -42.30)
>DroEre_CAF1 54612 120 - 1
ACAGGGGAAUCCCGUAUUCGUUCACGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGAAGCGGCGAUUUAAUUGCUGCGGCAGUCUGGCGAUUGACUGGGUAACUCAGGCUGCGAACCGA
...((.(((((((((........)).))))))).(((.(((((.((((((.........((((((((...))))))))..(((((........))))).))))))))))).)))..)).. ( -47.60)
>DroYak_CAF1 26228 120 - 1
ACGGGGGAAUCCCGUAUUCGUUUACGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGGAACGGCGACUUAAUUGCUGCGGCAGUCUGACGAUUGACUGGGCAACUCAGACUGUGAACCAA
(((((.....)))))....((((((((((((...((((((..((((((.((....)).)))(....).....))).)))))))))).........((((....).))).))))))))... ( -41.40)
>consensus
ACGGGGGAAUCCCGUAUUCGUUUACGGGGAUUUAUGCCGCCUGCAGUUGCAUAAUUGGAACGGCGAUUUAAUUGCUGCGGCAGUCUGACGAUUGACUGGGUAACUCAGUCUGUGAACC__
.((((.((((((((((......))).))))))).((((((..(((((((...(((((......)))))))))))).)))))).)))).((...(((((((...)))))))..))...... (-38.78 = -38.78 +   0.00)

alignment

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secondary structure

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Window 1

Location 21,076,776 – 21,076,895
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.21
Mean single sequence MFE -34.67
Consensus MFE -29.17
Energy contribution -29.19
Covariance contribution 0.02
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.84
SVM decision value 1.00
SVM RNA-class probability 0.897002
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21076776 119 + 23771897
CCGCAGCAAUUAAAUCGCCGUUCCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCAUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGUUGCACCGAAA-A
..((.((.........)).))........(((((((((((.((((((.((((((.............))))))...((((......)))).)))))...).)))))))))))......-. ( -37.32)
>DroSec_CAF1 131945 119 + 1
CCGCAGCAAUUAAAUCGCCGUUCCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCAUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA-A
..(((((.........((((((.......(((....)))))))))................(((.(((((.....))))).)))(((.((....)).)))))))).((....))....-. ( -34.01)
>DroSim_CAF1 38225 119 + 1
CCGCAGCAAUUAAAUCGCCGUUCCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA-A
..(((((.........(((..........(((....))))))(((((.....((((((......))))))......((((......)))).)))))....))))).((....))....-. ( -36.20)
>DroEre_CAF1 54652 107 + 1
CCGCAGCAAUUAAAUCGCCGCUUCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCGUGAACGAAUACGGGAUUCCCCUGUUUUUCUGCGGCAUG-------------GCGCACCGAAAAA
((((((..........((((((.......(((....))))))))).......((((((......))))))..............))))))..((-------------(....)))..... ( -31.11)
>DroYak_CAF1 26268 119 + 1
CCGCAGCAAUUAAGUCGCCGUUCCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUACAGGCGCACCGAAA-A
((((((.......((((((..........(((....))))))))).......((((((......))))))..............))))))...((((........)))).........-. ( -34.70)
>consensus
CCGCAGCAAUUAAAUCGCCGUUCCAAUUAUGCAACUGCAGGCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA_A
((((((..........((((((.......(((....)))))))))................(((.(((((.....))))).)))))))))...((((........))))........... (-29.17 = -29.19 +   0.02)

alignment

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secondary structure

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Window 2

Location 21,076,816 – 21,076,935
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.04
Mean single sequence MFE -32.75
Consensus MFE -25.18
Energy contribution -25.60
Covariance contribution 0.42
Combinations/Pair 1.09
Mean z-score -1.69
Structure conservation index 0.77
SVM decision value 0.28
SVM RNA-class probability 0.665163
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21076816 119 + 23771897
GCGGCAUAAAUCCCCAUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGUUGCACCGAAA-AAAUCAAUUAAAUUCCAGUGGCAAGCUCGCCGUAUGAAAAU
(((((................(((.(((((.....)))))..)))...(((.((((.(.((.(((....)))))((..-...))............).)))).))).)))))........ ( -33.50)
>DroSec_CAF1 131985 119 + 1
GCGGCAUAAAUCCCCAUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA-AAAUCAAUUAAAUUCCAGUGGCAAGCUCGCCGUAUGAAAAU
(((((................(((.(((((.....)))))..)))...(((.((((.(.((.(((....)))))((..-...))............).)))).))).)))))........ ( -33.20)
>DroSim_CAF1 38265 119 + 1
GCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA-AAAUCAAUUAAAUUCCAGUGGCAAGCUCGCCGUAUGAAAAU
(((((.........((((...(((.(((((.....)))))..)))))))((.((((.(.((.(((....)))))((..-...))............).)))).))..)))))........ ( -34.70)
>DroEre_CAF1 54692 107 + 1
GCGGCAUAAAUCCCCGUGAACGAAUACGGGAUUCCCCUGUUUUUCUGCGGCAUG-------------GCGCACCGAAAAAAAUCAAUUAAAUUCCAGUGCCAAACUUGCCGUAUGAAAAU
((((....((((((((....)).....))))))...))))((((((((((((((-------------((((...(((..............)))..))))))....))))))).))))). ( -30.34)
>DroYak_CAF1 26308 119 + 1
GCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUACAGGCGCACCGAAA-AAAUCAAUUAAAUUCCAGUGGCAAACUCGCCGUAUGAAAAU
(((((.......((((((......))))))........((((..(((.((....)).)))(((((.((....))((..-...))............)))))))))..)))))........ ( -32.00)
>consensus
GCGGCAUAAAUCCCCGUAAACGAAUACGGGAUUCCCCCGUUUUUCUGCGGCAUGCCUCAGGCUGCAGGCGCACCGAAA_AAAUCAAUUAAAUUCCAGUGGCAAGCUCGCCGUAUGAAAAU
((((....((((((.(((......)))))))))...))))(((((((((((..((((........))))((((.(((..............)))..))).)......)))))).))))). (-25.18 = -25.60 +   0.42)

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 13:01:42 2006