Locus 1683

Sequence ID 3L_DroMel_CAF1
Location 4,909,866 – 4,909,986
Length 120
Max. P 0.963320
window2594 window2595 window2596 window2597

overview

Window 4

Location 4,909,866 – 4,909,956
Length 90
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 77.97
Mean single sequence MFE -33.80
Consensus MFE -21.91
Energy contribution -23.80
Covariance contribution 1.89
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.65
SVM decision value 1.55
SVM RNA-class probability 0.963320
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4909866 90 + 23771897
AUGGGUGG-----------CU-----------CAAAAGUGGAAUGGCCAGCUG-------GUUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
..(..(.(-----------((-----------(((.(((((.....))).)).-------.)))))).)..)(.((((((((((......))))))))))).....((((....)))). ( -33.10)
>DroVir_CAF1 168245 79 + 1
AAGGGGGG----------------------------GGGGGGGUGGGCAGCAC-------AGCGGGCGG-----GCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAACGAG
.....(..----------------------------(..(.((..(((.((..-------.....)).(-----((((((((((......))))))))))))))..)).)..)..)... ( -29.40)
>DroSec_CAF1 131114 90 + 1
AUGGGUGG-----------UU-----------CAGAUGUGGAAUGGCCAGCUG-------GUUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
...(((.(-----------((-----------(.......)))).))).((((-------.((((((((..((.((((((((((......)))))))))))).))))).)))))))... ( -33.80)
>DroSim_CAF1 141122 90 + 1
AUGGGUGG-----------UU-----------CAGAUGUGGAAUGGCCAGCUG-------GUUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
...(((.(-----------((-----------(.......)))).))).((((-------.((((((((..((.((((((((((......)))))))))))).))))).)))))))... ( -33.80)
>DroEre_CAF1 132443 93 + 1
AUGG---------------CU-----------CAGAAGUGGGAUGGCCAGCUGUUGGGUUGUUGGGCGGCUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
..((---------------((-----------(((.(((.((....)).))).)))))))((((.(((((.((.((((((((((......))))))))))))...)))))..))))... ( -37.10)
>DroYak_CAF1 135255 114 + 1
AUGGGUGGUGCAAAAGUGGUGCAGAAGUGGUGCAAAAGUGGGUUGG-CAGCUGC----UUGUUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
..(((((((((....(((.(((....))).)))((((((.(.((((-..(((((----(.....)))))))))).).))))))............).)))))))).((((....)))). ( -35.60)
>consensus
AUGGGUGG___________UU___________CAGAAGUGGAAUGGCCAGCUG_______GUUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAG
..(((((................................(((.((.(((((.........))))).)).)))..((((((((((......))))))))))))))).((((....)))). (-21.91 = -23.80 +   1.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,909,866 – 4,909,956
Length 90
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 77.97
Mean single sequence MFE -20.38
Consensus MFE -15.99
Energy contribution -16.18
Covariance contribution 0.19
Combinations/Pair 1.06
Mean z-score -1.31
Structure conservation index 0.78
SVM decision value 0.76
SVM RNA-class probability 0.842422
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4909866 90 - 23771897
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAAC-------CAGCUGGCCAUUCCACUUUUG-----------AG-----------CCACCCAU
...((((..(((.....(((((.((((((......)))))).))).))...))).....-------))))((((((.........))-----------.)-----------)))..... ( -23.30)
>DroVir_CAF1 168245 79 - 1
CUCGUUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGC-----CCGCCCGCU-------GUGCUGCCCACCCCCCC----------------------------CCCCCCUU
...((.(.((((.(..((((((.((((((......)))))).)).-----))))..).)-------)))).))..........----------------------------........ ( -17.30)
>DroSec_CAF1 131114 90 - 1
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAAC-------CAGCUGGCCAUUCCACAUCUG-----------AA-----------CCACCCAU
...((((..(((.....(((((.((((((......)))))).))).))...))).....-------))))(((.....)))......-----------..-----------........ ( -18.50)
>DroSim_CAF1 141122 90 - 1
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAAC-------CAGCUGGCCAUUCCACAUCUG-----------AA-----------CCACCCAU
...((((..(((.....(((((.((((((......)))))).))).))...))).....-------))))(((.....)))......-----------..-----------........ ( -18.50)
>DroEre_CAF1 132443 93 - 1
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAGCCGCCCAACAACCCAACAGCUGGCCAUCCCACUUCUG-----------AG---------------CCAU
...(((((.((.....))((((.((((((......))))))..((....))))))..........)))))((((((.........))-----------.)---------------))). ( -23.40)
>DroYak_CAF1 135255 114 - 1
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAACAA----GCAGCUG-CCAACCCACUUUUGCACCACUUCUGCACCACUUUUGCACCACCCAU
...((((((((.....)))(((.((((((......)))))).)))................----)))))((-(.((......)).))).......((((.......))))........ ( -21.30)
>consensus
CUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAAC_______CAGCUGGCCAUCCCACUUCUG___________AA___________CCACCCAU
...((((.(((.....)))(((.((((((......)))))).))).....................))))................................................. (-15.99 = -16.18 +   0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,909,884 – 4,909,986
Length 102
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.96
Mean single sequence MFE -35.33
Consensus MFE -22.42
Energy contribution -23.58
Covariance contribution 1.17
Combinations/Pair 1.12
Mean z-score -2.03
Structure conservation index 0.63
SVM decision value 1.00
SVM RNA-class probability 0.898261
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4909884 102 + 23771897
GAAUGGCCAGCUG-------G-UUGGGCGGUUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAGACGCCGACAA-AGCGGCGUAAAUUUCAAUUA
((((.(((.....-------.-...))).))))(.((((((((((......))))))))))).....((((....)))).((((((....-..))))))............ ( -36.90)
>DroVir_CAF1 168257 97 + 1
GGGUGGGCAGCAC-------A-GCGGGCGG-----GCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAACGAGUCGCCGACAA-AGCGGCGUAAAUUUCAAUUA
...((.((.((..-------.-..((((((-----.(((((((((......)))))))))))))))((((((((.....)))).))))..-.)).)).))........... ( -36.60)
>DroGri_CAF1 167853 90 + 1
GUAG--------C-------A-GCGGGCGG-----GCGCGCUUUUCAAUGAUAAAAGUCGCCGCAUGUCGCGACAGCGAGACGCCGACAAAAGCGGCGUAAAUUUCAAUUA
((.(--------(-------.-(((.((((-----.((.((((((.......)))))))))))).))).)).))......((((((.(....)))))))............ ( -27.90)
>DroEre_CAF1 132457 109 + 1
GGAUGGCCAGCUGUUGGGUUG-UUGGGCGGCUCGAGCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAGACGCCGACAA-AACGGCGUAAAUUUCAAUUA
((....))....(((((((((-(((.(((((.((.((((((((((......))))))))))))...)))))..)))))).((((((....-..))))))....)))))).. ( -40.70)
>DroMoj_CAF1 177813 93 + 1
GGACGAGCGG------------UCGGGCGG-----UCGGCUUUUAAAAUGAUAAAAGUCGAGGCUUGUCGCGACAACGAGACGCCGACAA-AGCGGCGUAAAUUUCAAUUA
....((((((------------.(((((..-----((((((((((......)))))))))).))))))))).........((((((....-..)))))).....))..... ( -32.60)
>DroAna_CAF1 139335 109 + 1
GGGCGGCCUGGUGGUUGGAUGUUUGGGUGGU-UGGGCGGCUUUUAAAAUGAUAAAAGUCCCCGCUUGUCGCGACAGGGAGACGCCGACAA-AGCGGCGUAAAUUUCAAUUA
...(((((....)))))..((((..((..(.-((((.((((((((......)))))))))))).)..))..))))(..(.((((((....-..))))))...)..)..... ( -37.30)
>consensus
GGAUGGCCAGCUG_______G_UCGGGCGG_____GCGGCUUUUAAAAUGAUAAAAGUCGCCGCUUGUCGCGACAGCGAGACGCCGACAA_AGCGGCGUAAAUUUCAAUUA
.......................((((((......((((((((((......))))))))))))))))((((....)))).((((((.......))))))............ (-22.42 = -23.58 +   1.17)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,909,884 – 4,909,986
Length 102
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.96
Mean single sequence MFE -28.25
Consensus MFE -20.53
Energy contribution -21.25
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -1.58
Structure conservation index 0.73
SVM decision value 0.80
SVM RNA-class probability 0.853410
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4909884 102 - 23771897
UAAUUGAAAUUUACGCCGCU-UUGUCGGCGUCUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAACCGCCCAA-C-------CAGCUGGCCAUUC
...((((......(((((((-(.((((.((.(.....).)))))))))))))).((((((......))))))....))))...(((...-.-------.....)))..... ( -30.30)
>DroVir_CAF1 168257 97 - 1
UAAUUGAAAUUUACGCCGCU-UUGUCGGCGACUCGUUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGC-----CCGCCCGC-U-------GUGCUGCCCACCC
.............(((((((-(.((((.((((.....)))))))))))))))).((((((......))))))..((-----.(((....-.-------)))..))...... ( -31.90)
>DroGri_CAF1 167853 90 - 1
UAAUUGAAAUUUACGCCGCUUUUGUCGGCGUCUCGCUGUCGCGACAUGCGGCGACUUUUAUCAUUGAAAAGCGCGC-----CCGCCCGC-U-------G--------CUAC
.............((((((...(((((.((.(.....).))))))).))))))................((((((.-----.....)))-.-------)--------)).. ( -28.40)
>DroEre_CAF1 132457 109 - 1
UAAUUGAAAUUUACGCCGUU-UUGUCGGCGUCUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGCUCGAGCCGCCCAA-CAACCCAACAGCUGGCCAUCC
..............((((((-((((.((((.((((....(((.....)))(((.((((((......)))))).))).)))).))))..)-)))......))).)))..... ( -30.00)
>DroMoj_CAF1 177813 93 - 1
UAAUUGAAAUUUACGCCGCU-UUGUCGGCGUCUCGUUGUCGCGACAAGCCUCGACUUUUAUCAUUUUAAAAGCCGA-----CCGCCCGA------------CCGCUCGUCC
............(((..((.-..(((((.(((.((....)).)))..((.(((.((((((......)))))).)))-----..))))))------------).)).))).. ( -21.50)
>DroAna_CAF1 139335 109 - 1
UAAUUGAAAUUUACGCCGCU-UUGUCGGCGUCUCCCUGUCGCGACAAGCGGGGACUUUUAUCAUUUUAAAAGCCGCCCA-ACCACCCAAACAUCCAACCACCAGGCCGCCC
..............((((((-(.((((.((.(.....).))))))))))((((.((((((......)))))).).))).-.......................)))..... ( -27.40)
>consensus
UAAUUGAAAUUUACGCCGCU_UUGUCGGCGUCUCGCUGUCGCGACAAGCGGCGACUUUUAUCAUUUUAAAAGCCGC_____CCGCCCAA_C_______CAGCUGGCCAUCC
.............(((((((..(((((.((.(.....).)))))))))))))).((((((......))))))....................................... (-20.53 = -21.25 +   0.72)

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 10:13:35 2006