Locus 1519

Sequence ID 3L_DroMel_CAF1
Location 4,399,781 – 4,399,920
Length 139
Max. P 0.927656
window2362 window2363 window2364 window2365

overview

Window 2

Location 4,399,781 – 4,399,880
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 85.95
Mean single sequence MFE -19.63
Consensus MFE -15.01
Energy contribution -15.81
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.76
SVM decision value 1.18
SVM RNA-class probability 0.927656
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4399781 99 + 23771897
UUCACUUUCGCAAUCGAAUUCGAAAGCCCAUUUGCAUUGAUUUCGCUUGAGCUAUAUAU---UGUAUUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAU
.........((((.......(....).....))))((((...(((((((.(((((((..---..........)))))))...)))))))..))))....... ( -20.50)
>DroSec_CAF1 49708 94 + 1
UUCACUUUCGCAAUCGAAUUCGAAAGCCCAUUUGCAUUGAUUUCGCUUGAGCUAUAUA--------UUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAU
.........((((.......(....).....))))((((...(((((((.(((((((.--------......)))))))...)))))))..))))....... ( -21.30)
>DroSim_CAF1 50923 94 + 1
UUCACUUUUGCAAUCGAAUUCGAAAGCCCAUUUGCAUUGAUUUCGCUUGAGCUAUAUA--------UUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAU
.........((((.......(....).....))))((((...(((((((.(((((((.--------......)))))))...)))))))..))))....... ( -21.00)
>DroEre_CAF1 51832 94 + 1
UUCACUUUCGCAAUCGAAUUUGAAUGGUCAUUUGCAUUGAUUUCGCUGGAGCUAUAU--------AUUUAUAAUAUAGCAUGGAAGUGAUGCAAUAAAAAAU
.(((((((((((..((((..(.((((........)))).).)))).))..(((((((--------.......))))))).)))))))))............. ( -20.60)
>DroYak_CAF1 52899 89 + 1
UUCACUUUCGCAAUCGAAU-------------UGCAUUGAUUUCGCUUGAGCUAUAUACAUACAUACUUAUAAUAAAGCAUCGAAGUGAUGCAAUAAAAAAU
.........(((((...))-------------)))((((...(((((((((((.(((...............))).))).)).))))))..))))....... ( -14.76)
>consensus
UUCACUUUCGCAAUCGAAUUCGAAAGCCCAUUUGCAUUGAUUUCGCUUGAGCUAUAUA_______AUUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAU
.........((((..................))))((((...(((((((((((((((...............))))))).)).))))))..))))....... (-15.01 = -15.81 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,399,781 – 4,399,880
Length 99
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 85.95
Mean single sequence MFE -19.58
Consensus MFE -13.70
Energy contribution -14.70
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.70
SVM decision value 0.23
SVM RNA-class probability 0.645158
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4399781 99 - 23771897
AUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAAUACA---AUAUAUAGCUCAAGCGAAAUCAAUGCAAAUGGGCUUUCGAAUUCGAUUGCGAAAGUGAA
((((((..(((((((.(((((..(((((((..........---..)))))))))))).))......)))))....((..(((....)))..))))))))... ( -21.10)
>DroSec_CAF1 49708 94 - 1
AUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAA--------UAUAUAGCUCAAGCGAAAUCAAUGCAAAUGGGCUUUCGAAUUCGAUUGCGAAAGUGAA
((((((..(((((((.(((((..(((((((......--------.)))))))))))).))......)))))....((..(((....)))..))))))))... ( -21.90)
>DroSim_CAF1 50923 94 - 1
AUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAA--------UAUAUAGCUCAAGCGAAAUCAAUGCAAAUGGGCUUUCGAAUUCGAUUGCAAAAGUGAA
((((((..(((((((.(((((..(((((((......--------.)))))))))))).))......)))))....((..(((....)))..))))))))... ( -21.50)
>DroEre_CAF1 51832 94 - 1
AUUUUUUAUUGCAUCACUUCCAUGCUAUAUUAUAAAU--------AUAUAGCUCCAGCGAAAUCAAUGCAAAUGACCAUUCAAAUUCGAUUGCGAAAGUGAA
.............((((((.(..(((((((.......--------)))))))...............((((.(((..........))).))))).)))))). ( -16.90)
>DroYak_CAF1 52899 89 - 1
AUUUUUUAUUGCAUCACUUCGAUGCUUUAUUAUAAGUAUGUAUGUAUAUAGCUCAAGCGAAAUCAAUGCA-------------AUUCGAUUGCGAAAGUGAA
.......(((((((...((((..(((.(((((((......)))).))).))).....))))....)))))-------------))....(..(....)..). ( -16.50)
>consensus
AUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAAU_______UAUAUAGCUCAAGCGAAAUCAAUGCAAAUGGGCUUUCGAAUUCGAUUGCGAAAGUGAA
........(((((((.((((...(((((((...............))))))).)))).))......)))))..................(..(....)..). (-13.70 = -14.70 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,399,821 – 4,399,920
Length 99
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 87.66
Mean single sequence MFE -20.69
Consensus MFE -16.20
Energy contribution -16.20
Covariance contribution -0.00
Combinations/Pair 1.14
Mean z-score -1.69
Structure conservation index 0.78
SVM decision value 0.42
SVM RNA-class probability 0.728301
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4399821 99 + 23771897
UUUCGCUUGAGCUAUAUAU---UGUAUUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAUAAUUGCUAUCAUUUUGUGGGGAACUUGUCGUUUGCGUUUU
...(((.((((((((((..---..........))))))).(((((((((((((((........))))).))))))...)))).......)))...))).... ( -21.80)
>DroSec_CAF1 49748 94 + 1
UUUCGCUUGAGCUAUAUA--------UUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAUAAUUGCCAUCCUUUUGUAGGGAACUUGUCGUUUGCGUUUU
...(((.((((((((((.--------......)))))))...(((((...(((((........)))))..(((((....)))))))))))))...))).... ( -22.50)
>DroSim_CAF1 50963 94 + 1
UUUCGCUUGAGCUAUAUA--------UUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAUAAUUGCCAUCCUUUUGUAGGGAACUUGUCGUUUGCGUUUU
...(((.((((((((((.--------......)))))))...(((((...(((((........)))))..(((((....)))))))))))))...))).... ( -22.50)
>DroEre_CAF1 51872 94 + 1
UUUCGCUGGAGCUAUAU--------AUUUAUAAUAUAGCAUGGAAGUGAUGCAAUAAAAAAUAAUUGCCAUCCUUGUGUGGGCAACUUCUCUUUUGUGUUUU
...(((.((((((((((--------.......)))))))...(((((...(((((........)))))..(((......)))..))))))))...))).... ( -19.30)
>DroYak_CAF1 52926 102 + 1
UUUCGCUUGAGCUAUAUACAUACAUACUUAUAAUAAAGCAUCGAAGUGAUGCAAUAAAAAAUAAUUGCCAUCCUUAUGUAGAGAACUGCUCUUUUGUGUUUU
...(((..((((........(((((.(((......))).....(((.((((((((........)))).)))))))))))).......))))....))).... ( -17.36)
>consensus
UUUCGCUUGAGCUAUAUA_______AUUUAUAAUAUAGCAUCCAAGUGAUGCAAUAAAAAAUAAUUGCCAUCCUUUUGUAGGGAACUUGUCGUUUGCGUUUU
...(((.((((((((((...............)))))))...(((((...(((((........)))))..(((((....)))))))))))))...))).... (-16.20 = -16.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,399,821 – 4,399,920
Length 99
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 87.66
Mean single sequence MFE -20.36
Consensus MFE -14.24
Energy contribution -14.76
Covariance contribution 0.52
Combinations/Pair 1.04
Mean z-score -2.81
Structure conservation index 0.70
SVM decision value 1.17
SVM RNA-class probability 0.926161
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4399821 99 - 23771897
AAAACGCAAACGACAAGUUCCCCACAAAAUGAUAGCAAUUAUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAAUACA---AUAUAUAGCUCAAGCGAAA
....(((......(((((............(((.(((((........)))))))))))))((.(((((((..........---..)))))))))..)))... ( -19.50)
>DroSec_CAF1 49748 94 - 1
AAAACGCAAACGACAAGUUCCCUACAAAAGGAUGGCAAUUAUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAA--------UAUAUAGCUCAAGCGAAA
....(((......(((((..(((.....)))...(((((........)))))...)))))((.(((((((......--------.)))))))))..)))... ( -22.80)
>DroSim_CAF1 50963 94 - 1
AAAACGCAAACGACAAGUUCCCUACAAAAGGAUGGCAAUUAUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAA--------UAUAUAGCUCAAGCGAAA
....(((......(((((..(((.....)))...(((((........)))))...)))))((.(((((((......--------.)))))))))..)))... ( -22.80)
>DroEre_CAF1 51872 94 - 1
AAAACACAAAAGAGAAGUUGCCCACACAAGGAUGGCAAUUAUUUUUUAUUGCAUCACUUCCAUGCUAUAUUAUAAAU--------AUAUAGCUCCAGCGAAA
........((((((.(((((((..(....)...))))))).))))))......((.((.....(((((((.......--------)))))))...)).)).. ( -16.90)
>DroYak_CAF1 52926 102 - 1
AAAACACAAAAGAGCAGUUCUCUACAUAAGGAUGGCAAUUAUUUUUUAUUGCAUCACUUCGAUGCUUUAUUAUAAGUAUGUAUGUAUAUAGCUCAAGCGAAA
...........((((.((....((((((..((((.((((........))))))))......((((((......)))))).)))))).)).))))........ ( -19.80)
>consensus
AAAACGCAAACGACAAGUUCCCUACAAAAGGAUGGCAAUUAUUUUUUAUUGCAUCACUUGGAUGCUAUAUUAUAAAU_______UAUAUAGCUCAAGCGAAA
....(((......(((((............(((.(((((........)))))))))))))((.(((((((...............)))))))))..)))... (-14.24 = -14.76 +   0.52)

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 10:09:43 2006