Locus 5454

Sequence ID 2L_DroMel_CAF1
Location 15,540,906 – 15,541,030
Length 124
Max. P 0.975951
window8657 window8658 window8659

overview

Window 7

Location 15,540,906 – 15,540,999
Length 93
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.25
Mean single sequence MFE -23.78
Consensus MFE -14.58
Energy contribution -14.08
Covariance contribution -0.50
Combinations/Pair 1.33
Mean z-score -1.81
Structure conservation index 0.61
SVM decision value 0.72
SVM RNA-class probability 0.832749
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15540906 93 + 22407834
-------------GGAGCUCUGUUUU-CUGUUAGCUGCAAUAAUUGUUUAUUGGCAGCAAUGGAUUUGAAUUGUUAUCGAUUGCAGUUGGAAAACAAUUAUAAAUGA
-------------(.((((.......-.....)))).).((((((((((.(..((.(((((.(((..........))).))))).))..).))))))))))...... ( -24.40)
>DroVir_CAF1 65553 97 + 1
---------GCUCUGCGUUUUGUUUUGCAU-GAAUUGCAAUAAUUGUUUAUUGGCAACAAUGGAUUUAAAUUGUUAUCGGCUGCAGCUGUGAAACAAUUAUGAAUGC
---------((....(((.((((((..(..-((...(((((....((((((((....))))))))....)))))..))(((....))))..))))))..)))...)) ( -25.00)
>DroGri_CAF1 54620 96 + 1
---------GCUCUCCACUUUGUUUUGCUG-GAAUUGCAAUAAUUGUUUAUUGACAACAAUGGAUUUAAAUUGUUAUCGGUUGCAGCUGUGAAGCAAUUAUGAAUA-
---------......((..(((((((((((-.(((((.(((((((((((((((....))))))))...)))))))..))))).))))...)))))))...))....- ( -20.70)
>DroEre_CAF1 48442 93 + 1
--------------GAGCUCUGUUUUGCUGUUGGCUGCAAUAAUUGUUUAUUGGCAGCAAUGGAUUUGAAUUGUUAUCGAUUGCAGCUGGAAAACAAUUAUAAAUAA
--------------......(((...((.....)).)))((((((((((.(..((.(((((.(((..........))).))))).))..).))))))))))...... ( -24.90)
>DroMoj_CAF1 67845 97 + 1
---------GCUCUGCGUUUUGUUUUGCAU-GAAUUGCAAUAAUUGUUUAUUGACAACAAUGGAUUUAAAUUGUUAUCGACUGCAGCUGUGAAACGAUUAUGAAUGC
---------.....((((((.....((((.-....))))((((((((((.((((.((((((........)))))).))))..((....)).)))))))))))))))) ( -20.60)
>DroPer_CAF1 96267 107 + 1
AGAUAUUUCGGUCCCAGUUUCGUUUUGCCGGCAACAGCAAUAAUUGUUUAUUGGCAGCAAUGGAUUUAAAUUGUUAUCGAUUGCAGGGGCGAAACAAUUACAAAUGG
.....(((((.((((..........(((((....)...(((((....)))))))))(((((.(((..........))).))))).)))))))))............. ( -27.10)
>consensus
_________GCUCUGAGCUUUGUUUUGCUG_GAACUGCAAUAAUUGUUUAUUGGCAACAAUGGAUUUAAAUUGUUAUCGAUUGCAGCUGUGAAACAAUUAUAAAUGA
....................((((((((......(((((((....(((....)))((((((........))))))....)))))))..))))))))........... (-14.58 = -14.08 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,540,906 – 15,540,999
Length 93
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -18.52
Consensus MFE -12.16
Energy contribution -12.75
Covariance contribution 0.59
Combinations/Pair 1.13
Mean z-score -2.57
Structure conservation index 0.66
SVM decision value 1.76
SVM RNA-class probability 0.975951
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15540906 93 - 22407834
UCAUUUAUAAUUGUUUUCCAACUGCAAUCGAUAACAAUUCAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCAGCUAACAG-AAAACAGAGCUCC-------------
..........((((((((...........((.......)).........(((((.(((((....)))))))))).....)-)))))))......------------- ( -16.00)
>DroVir_CAF1 65553 97 - 1
GCAUUCAUAAUUGUUUCACAGCUGCAGCCGAUAACAAUUUAAAUCCAUUGUUGCCAAUAAACAAUUAUUGCAAUUC-AUGCAAAACAAAACGCAGAGC---------
((.....(((((((((....((.((((..(((..........)))..)))).))....)))))))))(((((....-.)))))........)).....--------- ( -17.00)
>DroGri_CAF1 54620 96 - 1
-UAUUCAUAAUUGCUUCACAGCUGCAACCGAUAACAAUUUAAAUCCAUUGUUGUCAAUAAACAAUUAUUGCAAUUC-CAGCAAAACAAAGUGGAGAGC---------
-............((((((..........(((((((((........)))))))))............((((.....-..))))......))))))...--------- ( -18.90)
>DroEre_CAF1 48442 93 - 1
UUAUUUAUAAUUGUUUUCCAGCUGCAAUCGAUAACAAUUCAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCAGCCAACAGCAAAACAGAGCUC--------------
.......(((((((((....((.(((((.(((..........))).))))).))....)))))))))((((........))))..........-------------- ( -18.20)
>DroMoj_CAF1 67845 97 - 1
GCAUUCAUAAUCGUUUCACAGCUGCAGUCGAUAACAAUUUAAAUCCAUUGUUGUCAAUAAACAAUUAUUGCAAUUC-AUGCAAAACAAAACGCAGAGC---------
.....................((((....(((((((((........)))))))))............(((((....-.)))))........))))...--------- ( -18.60)
>DroPer_CAF1 96267 107 - 1
CCAUUUGUAAUUGUUUCGCCCCUGCAAUCGAUAACAAUUUAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCUGUUGCCGGCAAAACGAAACUGGGACCGAAAUAUCU
...........(((((((.(((.(((((.(((..........))).)))))((((....((((........))))...))))..........)))..)))))))... ( -22.40)
>consensus
GCAUUCAUAAUUGUUUCACAGCUGCAAUCGAUAACAAUUUAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCAAUUC_CAGCAAAACAAAACGCAGAGC_________
.......(((((((((....((.(((((.(((..........))).))))).))....)))))))))((((........))))........................ (-12.16 = -12.75 +   0.59)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,540,927 – 15,541,030
Length 103
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.16
Mean single sequence MFE -15.45
Consensus MFE -11.63
Energy contribution -11.49
Covariance contribution -0.14
Combinations/Pair 1.17
Mean z-score -1.23
Structure conservation index 0.75
SVM decision value 0.06
SVM RNA-class probability 0.566147
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15540927 103 - 22407834
CAUAAGUUUAACCCCCGGUAUUCACACUUGGUCAUUUAUAAUUGUUUUCCAACUGCAAUCGAUAACAAUUCAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCA
.............((.(((......))).))......((((((((((.......(((((.(((..........))).))))).......)))))))))).... ( -15.24)
>DroVir_CAF1 65578 95 - 1
CAUUCGCUUCAUUC-----GUUCGCU---CUGCAUUCAUAAUUGUUUCACAGCUGCAGCCGAUAACAAUUUAAAUCCAUUGUUGCCAAUAAACAAUUAUUGCA
..............-----.......---..(((...((((((((((....((.((((..(((..........)))..)))).))....))))))))))))). ( -14.40)
>DroPse_CAF1 97439 97 - 1
CAUGAUUC-GACUC-----GUUCACACUUGGCCAUUUGUAAUUGUUUCGCCCCUGCAAUCGAUAACAAUUUAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCU
........-.....-----..........(((.....((((((((((.......(((((.(((..........))).))))).......)))))))))).))) ( -13.94)
>DroEre_CAF1 48463 103 - 1
UUUGAGUUGAACCCCCGGAAUUCACACUUGGUUAUUUAUAAUUGUUUUCCAGCUGCAAUCGAUAACAAUUCAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCA
.(..(((((((((...))..)))).)))..)......((((((((((....((.(((((.(((..........))).))))).))....)))))))))).... ( -20.10)
>DroYak_CAF1 50619 103 - 1
CAUAAGUUGAGCCCCCGGAAUUCACACUUGAUCAUUUAUAAUUGUUUUCCAGCUGCAAUCGAUAACAAUUCAAAUCCAUUGAUGCCAAUAAACAAUUAUUGCA
..((((((((.((...))...))).))))).......((((((((((....((..((((.(((..........))).))))..))....)))))))))).... ( -15.10)
>DroPer_CAF1 96302 97 - 1
CAUGAUUC-GACUC-----GUUCACACUUGGCCAUUUGUAAUUGUUUCGCCCCUGCAAUCGAUAACAAUUUAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCU
........-.....-----..........(((.....((((((((((.......(((((.(((..........))).))))).......)))))))))).))) ( -13.94)
>consensus
CAUGAGUU_AACCC_____AUUCACACUUGGUCAUUUAUAAUUGUUUCCCAGCUGCAAUCGAUAACAAUUCAAAUCCAUUGCUGCCAAUAAACAAUUAUUGCA
.....................................((((((((((.......(((((.(((..........))).))))).......)))))))))).... (-11.63 = -11.49 +  -0.14)

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 11:44:35 2006