Locus 8416

Sequence ID 3R_DroMel_CAF1
Location 22,432,179 – 22,432,304
Length 125
Max. P 0.820321
window13550 window13551 window13552 window13553

overview

Window 0

Location 22,432,179 – 22,432,276
Length 97
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 84.21
Mean single sequence MFE -37.30
Consensus MFE -25.63
Energy contribution -25.22
Covariance contribution -0.41
Combinations/Pair 1.28
Mean z-score -2.74
Structure conservation index 0.69
SVM decision value 0.32
SVM RNA-class probability 0.687925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22432179 97 + 27905053
AAACUCGUCAAAGGGCCAUUGGAGCUGGGACAAUGAGUGGAUAGCUUGCAGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
............(((((((..((((((...((.....))..))))))(((.((((((((----------------(..(...--)..)).))))))).....))))))))))... ( -36.50)
>DroSec_CAF1 65712 97 + 1
AAACUCGUGAAAGGGCCAUUGGAGCUGGGACAAUGAGUGGAUAGCUUGCUGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
............(((((((..((((((...((.....))..))))))((..((((((((----------------(..(...--)..)).)))))))......)))))))))... ( -34.40)
>DroSim_CAF1 62103 97 + 1
AAACUCGUGAAAGGGCCAUUGGAGCUGGGACAAUGAGUGGAUAGCUUGCUGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
............(((((((..((((((...((.....))..))))))((..((((((((----------------(..(...--)..)).)))))))......)))))))))... ( -34.40)
>DroEre_CAF1 64122 113 + 1
AAACUCGGGAAAGGGCUAUUGGAGCAGGGACAAUGAGUGGAUAGCUCGCAGAUGGGCUGAUGGCUUGAUGGCCUGAUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
.....((((...((((((((.(..((.......))..).))))))))(((.((((((((..(((.....((((.....))))--..))))))))))).....)))....)))).. ( -42.40)
>DroYak_CAF1 63887 105 + 1
AAACUCGUGAAAGGGCCGUUGGAGCAGGGACAAUGAGUGGAUAGCUUGCAGAUGGGCUGAU--------GGCCUGAUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
............(((((((..((((..(..((.....))..).))))(((.((((((((((--------((((.....))))--..))).))))))).....))))))))))... ( -38.80)
>DroAna_CAF1 71379 97 + 1
AAUCCCAUGAAAAGGCCAUUGGUGAACAGACAAUGAGUGGCCAG--UGCGGAUGGGCUG----------------AUGGCCUGAUGGUCUGGGCCAUAAAAAUGCAUAGUCCGCA
.............(((((((.((.........)).)))))))..--(((((((..((..----------------(((((((........)))))))......))...))))))) ( -37.30)
>consensus
AAACUCGUGAAAGGGCCAUUGGAGCAGGGACAAUGAGUGGAUAGCUUGCAGAUGGGCUG________________AUGGGCU__UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCA
............(((((((((.........))))..(((..((((((......))))))................(((((((........))))))).......))))))))... (-25.63 = -25.22 +  -0.41)

alignment

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secondary structure

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Window 1

Location 22,432,179 – 22,432,276
Length 97
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 84.21
Mean single sequence MFE -27.42
Consensus MFE -20.23
Energy contribution -20.37
Covariance contribution 0.14
Combinations/Pair 1.19
Mean z-score -1.83
Structure conservation index 0.74
SVM decision value 0.03
SVM RNA-class probability 0.549647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22432179 97 - 27905053
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCUGCAAGCUAUCCACUCAUUGUCCCAGCUCCAAUGGCCCUUUGACGAGUUU
...((((((((((.....(((((((.((...--......)----------------)))))))).))).((((....((.....))...))))...)))))))............ ( -27.40)
>DroSec_CAF1 65712 97 - 1
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCAGCAAGCUAUCCACUCAUUGUCCCAGCUCCAAUGGCCCUUUCACGAGUUU
...(((((((........(((((((......--)))))))----------------..((......)).((((....((.....))...))))...)))))))............ ( -26.60)
>DroSim_CAF1 62103 97 - 1
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCAGCAAGCUAUCCACUCAUUGUCCCAGCUCCAAUGGCCCUUUCACGAGUUU
...(((((((........(((((((......--)))))))----------------..((......)).((((....((.....))...))))...)))))))............ ( -26.60)
>DroEre_CAF1 64122 113 - 1
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAUCAGGCCAUCAAGCCAUCAGCCCAUCUGCGAGCUAUCCACUCAUUGUCCCUGCUCCAAUAGCCCUUUCCCGAGUUU
.((((((...........(((((((......--)))))))..(((......)))....))))...((.((((.....((.....))....))))))...)).............. ( -29.90)
>DroYak_CAF1 63887 105 - 1
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAUCAGGCC--------AUCAGCCCAUCUGCAAGCUAUCCACUCAUUGUCCCUGCUCCAACGGCCCUUUCACGAGUUU
...(((((.((((.....(((((((.((...--.(((.....))).--------.))))))))).))))(((.....((.....))....))).....)))))............ ( -30.50)
>DroAna_CAF1 71379 97 - 1
UGCGGACUAUGCAUUUUUAUGGCCCAGACCAUCAGGCCAU----------------CAGCCCAUCCGCA--CUGGCCACUCAUUGUCUGUUCACCAAUGGCCUUUUCAUGGGAUU
((((((....((......((((((..........))))))----------------..))...))))))--..(((((.....((......))....)))))............. ( -23.50)
>consensus
UGCGGGCCAUGCAUUUUUAUGGGCUAGACAA__AGCCCAU________________CAGCCCAUCUGCAAGCUAUCCACUCAUUGUCCCAGCUCCAAUGGCCCUUUCACGAGUUU
...(((((((........(((((((........)))))))..................((......))............................)))))))............ (-20.23 = -20.37 +   0.14)

alignment

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secondary structure

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Window 2

Location 22,432,214 – 22,432,304
Length 90
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -34.07
Consensus MFE -24.36
Energy contribution -23.89
Covariance contribution -0.47
Combinations/Pair 1.25
Mean z-score -2.06
Structure conservation index 0.72
SVM decision value 0.27
SVM RNA-class probability 0.662111
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22432214 90 + 27905053
AGUGGAUAGCUUGCAGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGCUGCCCC-----C--GUU
...((...(((((((.((((((((----------------(..(...--)..)).))))))).....)))).)))..(((.((((((....)))))).)))..)-----)--... ( -30.50)
>DroSec_CAF1 65747 90 + 1
AGUGGAUAGCUUGCUGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGCUGCCCC-----C--GUU
.(.((.((((....((.((((((.----------------(((((((--......)))))))..........))))))))..(((((....))))))))).)).-----)--... ( -30.40)
>DroSim_CAF1 62138 90 + 1
AGUGGAUAGCUUGCUGAUGGGCUG----------------AUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGCUGCCCC-----C--GUU
.(.((.((((....((.((((((.----------------(((((((--......)))))))..........))))))))..(((((....))))))))).)).-----)--... ( -30.40)
>DroEre_CAF1 64157 106 + 1
AGUGGAUAGCUCGCAGAUGGGCUGAUGGCUUGAUGGCCUGAUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGAUGCCCC-----C--GUU
.((((.....))))....(((((...((((....))))..(((((((--......)))))))..........)))))((((((((((....))))))))))...-----.--... ( -41.10)
>DroYak_CAF1 63922 100 + 1
AGUGGAUAGCUUGCAGAUGGGCUGAU--------GGCCUGAUGGGCU--UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGCUGCCCC-----CCGGUU
..(((...(((((((.((((((((((--------((((.....))))--..))).))))))).....)))).)))..(((.((((((....)))))).)))...-----)))... ( -37.00)
>DroAna_CAF1 71414 95 + 1
AGUGGCCAG--UGCGGAUGGGCUG----------------AUGGCCUGAUGGUCUGGGCCAUAAAAAUGCAUAGUCCGCAUUGCAAUUUUGAUUGGACCACCUCUUUCCC--AUU
.((((.(((--(((((((..((..----------------(((((((........)))))))......))...))))))))))((((....))))..)))).........--... ( -35.00)
>consensus
AGUGGAUAGCUUGCAGAUGGGCUG________________AUGGGCU__UUGUCUAGCCCAUAAAAAUGCAUGGCCCGCAUUGCAAUUUUGAUUGCGCUGCCCC_____C__GUU
...((.............((((((................(((((((........))))))).........))))))(((.((((((....)))))).)))))............ (-24.36 = -23.89 +  -0.47)

alignment

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secondary structure

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Window 3

Location 22,432,214 – 22,432,304
Length 90
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -30.32
Consensus MFE -23.51
Energy contribution -23.60
Covariance contribution 0.09
Combinations/Pair 1.09
Mean z-score -2.30
Structure conservation index 0.78
SVM decision value 0.68
SVM RNA-class probability 0.820321
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22432214 90 - 27905053
AAC--G-----GGGGCAGCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCUGCAAGCUAUCCACU
...--.-----.((..((((((((....)))))..(((((((..((.......(((((((......--)))))))----------------))))))....))).)))..))... ( -29.11)
>DroSec_CAF1 65747 90 - 1
AAC--G-----GGGGCAGCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCAGCAAGCUAUCCACU
...--.-----.((..((((((((....)))))..(((((((..((.......(((((((......--)))))))----------------))))))....))).)))..))... ( -29.11)
>DroSim_CAF1 62138 90 - 1
AAC--G-----GGGGCAGCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAU----------------CAGCCCAUCAGCAAGCUAUCCACU
...--.-----.((..((((((((....)))))..(((((((..((.......(((((((......--)))))))----------------))))))....))).)))..))... ( -29.11)
>DroEre_CAF1 64157 106 - 1
AAC--G-----GGGGCAUCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAUCAGGCCAUCAAGCCAUCAGCCCAUCUGCGAGCUAUCCACU
..(--(-----.((((((.(((((....))))).))))((((...........(((((((......--)))))))..(((......)))....))))..)).))........... ( -36.00)
>DroYak_CAF1 63922 100 - 1
AACCGG-----GGGGCAGCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA--AGCCCAUCAGGCC--------AUCAGCCCAUCUGCAAGCUAUCCACU
...(((-----(((((.(((((((....)))))...)).((((.((.......(((((((......--)))))))))))))--------....)))).))))............. ( -32.91)
>DroAna_CAF1 71414 95 - 1
AAU--GGGAAAGAGGUGGUCCAAUCAAAAUUGCAAUGCGGACUAUGCAUUUUUAUGGCCCAGACCAUCAGGCCAU----------------CAGCCCAUCCGCA--CUGGCCACU
...--........(((((((((((....))))...((((((....((......((((((..........))))))----------------..))...))))))--..))))))) ( -25.70)
>consensus
AAC__G_____GGGGCAGCGCAAUCAAAAUUGCAAUGCGGGCCAUGCAUUUUUAUGGGCUAGACAA__AGCCCAU________________CAGCCCAUCUGCAAGCUAUCCACU
............((((...(((((....)))))((((((.....))))))...(((((((........)))))))..................)))).................. (-23.51 = -23.60 +   0.09)

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 13:10:58 2006