Locus 1373

Sequence ID 3L_DroMel_CAF1
Location 3,995,977 – 3,996,068
Length 91
Max. P 0.963688
window2136 window2137

overview

Window 6

Location 3,995,977 – 3,996,068
Length 91
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 77.87
Mean single sequence MFE -26.25
Consensus MFE -16.33
Energy contribution -16.82
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.11
Structure conservation index 0.62
SVM decision value 1.13
SVM RNA-class probability 0.919163
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3995977 91 + 23771897
UUU----CUU--------UUUUUUUCAAAAAGGGGCUGUUGCGUGGGCGGGGCAUUUAUUUUCGCCACCCAUUUUGUUUGUGGUGCGCUUUAUCAAACAGAAA
...----...--------.............(((((....))...((((..(.......)..)))).))).(((((((((.((....))....))))))))). ( -23.50)
>DroSec_CAF1 68577 89 + 1
UUU----GUU----------UUUUUCAAAAAGGGGCUGUGCCGGGGGCGGGGCAUUUAUUUUCGCCACCCAUUUUGUUUGUGGUGCGCUUUAUCAAACAGAAA
...----...----------.............(((...)))(((((((..(.......)..)))).))).(((((((((.((....))....))))))))). ( -25.40)
>DroEre_CAF1 71746 98 + 1
UUUUGUUGUUUUUUUCAUUUUUGUUCGGGAAAG----UGGGU-GGGGUGGCGCAUUUAUUUUCGCCACCCAUUUUGUUUGUGGUGCGCUUUAUCAAACAGAAA
.............(((((((((......)))))----)))).-.((((((((.(......).)))))))).(((((((((.((....))....))))))))). ( -28.40)
>DroYak_CAF1 73337 97 + 1
-----UUUUUUUUUAUAUUUUUGUUCACAAAGGGGAUGGGGU-GGGGUGGAGCAUUUAUUUUCGCCACCCAUUUUGUUUGUGGUGCGCUUUAUCAAACAGAAA
-----............((((((((((((((.((((((((..-..(((((((.......))))))).)))))))).))))))(....).......)))))))) ( -27.70)
>consensus
UUU____GUU________UUUUGUUCAAAAAGGGGCUGGGGC_GGGGCGGGGCAUUUAUUUUCGCCACCCAUUUUGUUUGUGGUGCGCUUUAUCAAACAGAAA
............................................((((((.(.(......).).)))))).(((((((((.((....))....))))))))). (-16.33 = -16.82 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 3,995,977 – 3,996,068
Length 91
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 77.87
Mean single sequence MFE -17.39
Consensus MFE -12.97
Energy contribution -12.72
Covariance contribution -0.25
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 1.56
SVM RNA-class probability 0.963688
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3995977 91 - 23771897
UUUCUGUUUGAUAAAGCGCACCACAAACAAAAUGGGUGGCGAAAAUAAAUGCCCCGCCCACGCAACAGCCCCUUUUUGAAAAAAA--------AAG----AAA
....((((((.............))))))...(((((((.(...........)))))))).((....))..((((((.....)))--------)))----... ( -16.82)
>DroSec_CAF1 68577 89 - 1
UUUCUGUUUGAUAAAGCGCACCACAAACAAAAUGGGUGGCGAAAAUAAAUGCCCCGCCCCCGGCACAGCCCCUUUUUGAAAAA----------AAC----AAA
((((((((((.............))))))....(((.((((.............)))))))(((...))).......))))..----------...----... ( -17.34)
>DroEre_CAF1 71746 98 - 1
UUUCUGUUUGAUAAAGCGCACCACAAACAAAAUGGGUGGCGAAAAUAAAUGCGCCACCCC-ACCCA----CUUUCCCGAACAAAAAUGAAAAAAACAACAAAA
....((((((..((((.(.....).........((((((((..........)))))))).-.....----))))..))))))..................... ( -20.10)
>DroYak_CAF1 73337 97 - 1
UUUCUGUUUGAUAAAGCGCACCACAAACAAAAUGGGUGGCGAAAAUAAAUGCUCCACCCC-ACCCCAUCCCCUUUGUGAACAAAAAUAUAAAAAAAAA-----
.....((((....))))....((((((......((((((.(................)))-)))).......))))))....................----- ( -15.31)
>consensus
UUUCUGUUUGAUAAAGCGCACCACAAACAAAAUGGGUGGCGAAAAUAAAUGCCCCACCCC_ACCACAGCCCCUUUUUGAAAAAAA________AAC____AAA
.(((((((((.............))))))....((((((.(..........).))))))..................)))....................... (-12.97 = -12.72 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:54 2006