Locus 2066

Sequence ID 3L_DroMel_CAF1
Location 5,683,987 – 5,684,108
Length 121
Max. P 0.978284
window3219 window3220 window3221

overview

Window 9

Location 5,683,987 – 5,684,079
Length 92
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 74.41
Mean single sequence MFE -21.90
Consensus MFE -12.66
Energy contribution -12.05
Covariance contribution -0.61
Combinations/Pair 1.25
Mean z-score -2.19
Structure conservation index 0.58
SVM decision value 1.81
SVM RNA-class probability 0.978284
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5683987 92 + 23771897
CUUGCUACUCCUGCCUUU-CAA-CC-----------CACCGCCUCCCC----------UCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAGCUCUCUGC
.((((((.....(((.((-(((-..-----------....((.((...----------..)).)).......))).)).))).((((......))))....))))))........ ( -15.52)
>DroPse_CAF1 60308 103 + 1
CUUGCUGCCUCUGCCCUCGCCC-CC-----------CACGGACCCCUGUCCGUGCCUUCUGCUGCUUUCAAUUUGCAAUGGCGGCUGUCAUUUCAGCUCAAUAGCAGCUCUAUCU
...(((((.........((((.-..-----------(((((((....)))))))........(((.........)))..))))((((......))))......)))))....... ( -32.20)
>DroSec_CAF1 56529 83 + 1
CUUGCUACUCCUCCCUUU-CAA-CC-----------CACCGACUCCCC----------UCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCA---------
..(((((...........-...-.(-----------((.(((......----------))).(((.........))).)))..((((......))))....)))))--------- ( -13.70)
>DroEre_CAF1 60008 98 + 1
CUUGCUACUCCUGCUCUU-CAG-CCCGGC-----CCCACCAACGCCCC----------UCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAACUCACUGC
.((((((...........-.((-((.(((-----.........)))..----------....(((.........)))..))))((((......))))....))))))........ ( -20.00)
>DroYak_CAF1 58190 103 + 1
CUUGCUACUCCCGCUUUU-CAG-CCCAACCGCCCCCCACCGACGCCCC----------UCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAGCUCACUGC
.((((((...........-.((-((..............(((......----------))).(((.........)))..))))((((......))))....))))))........ ( -18.40)
>DroPer_CAF1 60864 104 + 1
CUUGCUGCCUCUGCCCUCGCCCCCC-----------CACGGGCCCCUGUCCGUGCCUUCUGCUGCUUUCAAUUUGCAAUGGCGGCUGUCAUUUCAGCUCAAUAGCAGCUCUCUCU
...(((((.........((((....-----------(((((((....)))))))........(((.........)))..))))((((......))))......)))))....... ( -31.60)
>consensus
CUUGCUACUCCUGCCCUU_CAA_CC___________CACCGACCCCCC__________UCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAGCUCUCUGC
.((((((...................................................(((.(((.........))).)))..((((......))))....))))))........ (-12.66 = -12.05 +  -0.61)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,683,987 – 5,684,079
Length 92
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.41
Mean single sequence MFE -29.63
Consensus MFE -14.93
Energy contribution -14.73
Covariance contribution -0.19
Combinations/Pair 1.25
Mean z-score -2.04
Structure conservation index 0.50
SVM decision value 1.07
SVM RNA-class probability 0.909579
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5683987 92 - 23771897
GCAGAGAGCUGCUAUUGAGCUGAAAUGACAGCAGCCAUUGCAAAUUGAAAGCAUCGA----------GGGGAGGCGGUG-----------GG-UUG-AAAGGCAGGAGUAGCAAG
.......((((((.(((.((((......))))..(((((((...((((.....))))----------......))))))-----------).-...-.....))).))))))... ( -26.90)
>DroPse_CAF1 60308 103 - 1
AGAUAGAGCUGCUAUUGAGCUGAAAUGACAGCCGCCAUUGCAAAUUGAAAGCAGCAGAAGGCACGGACAGGGGUCCGUG-----------GG-GGGCGAGGGCAGAGGCAGCAAG
.......((((((.(((.((((......))))((((.((((.........)))).......(((((((....)))))))-----------..-.))))....))).))))))... ( -38.00)
>DroSec_CAF1 56529 83 - 1
---------UGCUAUUGAGCUGAAAUGACAGCAGCCAUUGCAAAUUGAAAGCAUCGA----------GGGGAGUCGGUG-----------GG-UUG-AAAGGGAGGAGUAGCAAG
---------(((((((..((((......))))..((.((.(...((.((..((((((----------......))))))-----------..-)).-)).).))))))))))).. ( -20.50)
>DroEre_CAF1 60008 98 - 1
GCAGUGAGUUGCUAUUGAGCUGAAAUGACAGCAGCCAUUGCAAAUUGAAAGCAUCGA----------GGGGCGUUGGUGGG-----GCCGGG-CUG-AAGAGCAGGAGUAGCAAG
........((((((((..((((......)))).((((.(((...((((.....))))----------...))).))))...-----.((..(-((.-...))).)))))))))). ( -28.70)
>DroYak_CAF1 58190 103 - 1
GCAGUGAGCUGCUAUUGAGCUGAAAUGACAGCAGCCAUUGCAAAUUGAAAGCAUCGA----------GGGGCGUCGGUGGGGGGCGGUUGGG-CUG-AAAAGCGGGAGUAGCAAG
((..(.(((((((.....((((......)))).(((..(((...((((.....))))----------...)))..)))....))))))).)(-((.-...))).......))... ( -30.20)
>DroPer_CAF1 60864 104 - 1
AGAGAGAGCUGCUAUUGAGCUGAAAUGACAGCCGCCAUUGCAAAUUGAAAGCAGCAGAAGGCACGGACAGGGGCCCGUG-----------GGGGGGCGAGGGCAGAGGCAGCAAG
.......((((((.(((.((((......))))((((.((((.........)))).......(((((........)))))-----------....))))....))).))))))... ( -33.50)
>consensus
GCAGAGAGCUGCUAUUGAGCUGAAAUGACAGCAGCCAUUGCAAAUUGAAAGCAUCGA__________GGGGAGUCGGUG___________GG_CUG_AAAGGCAGGAGUAGCAAG
.......((((((.(((.((((......))))......(((.........))).................................................))).))))))... (-14.93 = -14.73 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,684,014 – 5,684,108
Length 94
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 70.47
Mean single sequence MFE -19.47
Consensus MFE -10.67
Energy contribution -10.67
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.55
SVM decision value 1.67
SVM RNA-class probability 0.971346
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5684014 94 + 23771897
GCCUCCCCUCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAG-----CUCUCUGCAGUCCUCCCAAACC-AGCCAU-GCCACGCCC---
((.((.....)).)).........(((.(((((((((......))))......((((-----....))))..............-))))))-)).......--- ( -20.90)
>DroVir_CAF1 70544 81 + 1
--------CUGCUGCUUUCAAUUUGCAAUGGCGGCUGUCAUUUCAGCUCAAUAGCAG-----CC----CCC----ACCCACAACCACCCCCGGCCAUGCCCA--
--------..((((((......(((.((((((....)))))).)))......)))))-----).----...----................(((...)))..-- ( -17.80)
>DroEre_CAF1 60041 92 + 1
AACGCCCCUCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAA-----CUCACUGCCGUC---CCACUCC-AGCCAC-GCCACGCCCA--
...((....((.(((.........))).(((((((((......))))......(((.-----.....)))....---.......-))))))-)....))...-- ( -16.90)
>DroWil_CAF1 72510 81 + 1
--------CUGCUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAG-----CUCCAUUCCAUC---UCCAUCU-GGUC----C--CCCCAACC
--------..((((((......(((.((((((....)))))).)))......)))))-----)...........---......(-((..----.--..)))... ( -18.20)
>DroYak_CAF1 58228 92 + 1
GACGCCCCUCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAG-----CUCACUGCAGCC---UCACUCC-CGGCAU-GCCACGCCCA--
((.((.....((.....))....((((.((((((((((............)))))))-----).)).)))))).---)).....-.(((..-.....)))..-- ( -23.10)
>DroAna_CAF1 58017 90 + 1
-----CCCCGGUUGCUUUCAAUUUGCAAUGGCUCCUGUCAUUUCAGCUCAAUAGCAGUAGAGCCUACUGC--UC---CUCCUCC-UGCCAC-GCCCUCUCAA--
-----....((((((.........))).((((..(((......)))......((((((((...)))))))--).---.......-.)))).-))).......-- ( -19.90)
>consensus
_____CCCCCGAUGCUUUCAAUUUGCAAUGGCUGCUGUCAUUUCAGCUCAAUAGCAG_____CUCACUGCCGUC___CCACUCC_AGCCAC_GCCACGCCCA__
............((((......(((.((((((....)))))).)))......))))................................................ (-10.67 = -10.67 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:35 2006