Locus 1447

Sequence ID 3L_DroMel_CAF1
Location 4,184,528 – 4,184,662
Length 134
Max. P 0.717766
window2254 window2255 window2256

overview

Window 4

Location 4,184,528 – 4,184,640
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.15
Mean single sequence MFE -32.40
Consensus MFE -15.38
Energy contribution -15.38
Covariance contribution 0.00
Combinations/Pair 1.30
Mean z-score -2.33
Structure conservation index 0.47
SVM decision value 0.12
SVM RNA-class probability 0.593995
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4184528 112 - 23771897
AAGGGCGUCUUCGACACGACGCUGUUCAAGAGUCCCCUCAGCGAUAGGGAGAUGGAGAGAAAUC------UCCAUGGGCUGCGUCAGAACUUGCCAAAAAAUCAUAAACUAUUCUGAA--
...((((..(((.....(((((.(((((...(((((((.......)))).)))(((((....))------))).))))).))))).)))..)))).......................-- ( -37.40)
>DroVir_CAF1 33639 114 - 1
AAAGGCGUCUUUGACACGACGCUCUUCAAGAGUCCCCUCAGCGAUCGGGAAAUGGAUCGUAAGC------UCCAUUUGCUGCGUCAGAACUUGCCAAAAAAUCAUAAACUAUAUUAAAAU
...((((..((((((.(((((((......(((....))))))).)))(.(((((((.(....).------))))))).)...))))))...))))......................... ( -31.30)
>DroGri_CAF1 35427 112 - 1
AAAGGCAUCUUCGAUACGACGCUCUUCAAAAGUCCCCAGAGCGAUCGGGAAAUGGAGCGCCAAC------UCCACGCCCUGCGUCAGAAUUUGCCAAAAAAUCACAAACUAUAUUAAA--
...((((..(((((..(((((((((............)))))).))(((...(((((......)------))))..))).)..)).)))..)))).......................-- ( -31.60)
>DroMoj_CAF1 33750 114 - 1
AAAGGCAUCUUCGAUACGACGCUCUUCAAGACUCCCCAGAGCGAUCGCGAAAUGGAGAGAAAGC------UCCUCGCGCUACGUCAGAACUUGCCAAAAAAUCACAAACUAUAUUAACAG
...((((..(((...(((.((((((............))))))..(((((...((((......)------))))))))...)))..)))..))))......................... ( -30.80)
>DroAna_CAF1 31288 112 - 1
AAGGGUGUGUUCGACACCACCUUGUUCAAGAGCCCGCUCAGCGACAGGGAGAUGGAGCGGAAGC------UCCAUGGACUGCGUCAGAACUUGCCAAAAAACCACAAACUGUACUGAC--
...((((.(((((((....(((((((...(((....)))...)))))))..(((((((....))------))))).......))).)))).)))).......................-- ( -38.60)
>DroPer_CAF1 31711 118 - 1
AAAGGCGUCUUUGACACGACGCUCUUCAAGAGCCCGCACAGCGACAGGGAGAUGGAAAGGAACCGGAACAUCCAUGUGCUCCGCCAGAACUUGCCAAAAAACCACAAACUAUACUAAA--
...((((..((((.......((((.....))))..((..(((.(((.(((..(((.......))).....))).))))))..))))))...)))).......................-- ( -24.70)
>consensus
AAAGGCGUCUUCGACACGACGCUCUUCAAGAGUCCCCACAGCGAUAGGGAAAUGGAGAGAAAGC______UCCAUGCGCUGCGUCAGAACUUGCCAAAAAAUCACAAACUAUACUAAA__
...((((..((((((....(((((..............)))))........(((((..............))))).......))).)))..))))......................... (-15.38 = -15.38 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,184,566 – 4,184,662
Length 96
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 83.44
Mean single sequence MFE -38.40
Consensus MFE -26.40
Energy contribution -26.77
Covariance contribution 0.37
Combinations/Pair 1.35
Mean z-score -2.47
Structure conservation index 0.69
SVM decision value 0.39
SVM RNA-class probability 0.717766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4184566 96 + 23771897
AGCCCAUGGAGAUUUCUCUCCAUCUCCCUAUCGCUGAGGGGACUCUUGAACAGCGUCGUGUCGAAGACGCCCUUAGUAGUCCGCUUGGAUGUGGA-U--
.....(((((((....)))))))....((((..(..((.(((((.((((...(((((........)))))..)))).))))).))..)..)))).-.-- ( -35.00)
>DroVir_CAF1 33679 99 + 1
AGCAAAUGGAGCUUACGAUCCAUUUCCCGAUCGCUGAGGGGACUCUUGAAGAGCGUCGUGUCAAAGACGCCUUUCGUGGUGCGCUUCGGCGUCGGGUUU
...(((((((........)))))))(((((.(((((((((.(((..(((((.(((((........))))).))))).))).).)))))))))))))... ( -44.20)
>DroGri_CAF1 35465 99 + 1
AGGGCGUGGAGUUGGCGCUCCAUUUCCCGAUCGCUCUGGGGACUUUUGAAGAGCGUCGUAUCGAAGAUGCCUUUGGUGGUGCGCUUCAGUGUCGGAUUU
.(((.(((((((....))))))).)))(((.((((..(((.(((.(..(((.(((((........))))))))..).))).).))..)))))))..... ( -37.10)
>DroSec_CAF1 30254 96 + 1
AGCCCAUGGAGAUUUCUCUCCAUCUCCCGAUCGCUGAGGGGACUCUUGAACAGCGUCGUGUCGAAGACGCCCUUAGUGGUCCGCUUAGAUGUGGG-U--
.(((((((((((....)))))((((.(.(((((((((((.(((.((.....)).)))(((((...)))))))))))))))).)...)))))))))-)-- ( -39.90)
>DroEre_CAF1 30699 96 + 1
ACCCCAUGGAGAUUUCUCUCCAAUUCUCGAUCACUGAGGGGACUCUUGAACAGCGUCGUGUCGAAGACGCCCUUAGUGGUUCGCUUGGAUGUGGG-U--
..((((((((((....))))).((((.((((((((((((.(((.((.....)).)))(((((...)))))))))))))).)))...)))))))))-.-- ( -37.60)
>DroYak_CAF1 34738 96 + 1
AGCCCAUGGAGAUUUCUCUCCAUUUCUCGAUCACUGAGGGGACUCUUGAACAGCGUCGUAUCGAAGACGCCCUUGGUGGUUCGCUUGGAUGUGGG-U--
.(((((((((((....)))))...((((((((((..((((..(....)..).(((((........))))))))..)))).)))...))).)))))-)-- ( -36.60)
>consensus
AGCCCAUGGAGAUUUCUCUCCAUUUCCCGAUCGCUGAGGGGACUCUUGAACAGCGUCGUGUCGAAGACGCCCUUAGUGGUCCGCUUGGAUGUGGG_U__
.....(((((((....)))))))..(((...(((((((.(((((.((((...(((((........)))))..)))).))))).))))).)).))).... (-26.40 = -26.77 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,184,566 – 4,184,662
Length 96
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 83.44
Mean single sequence MFE -32.40
Consensus MFE -20.29
Energy contribution -20.60
Covariance contribution 0.31
Combinations/Pair 1.28
Mean z-score -2.20
Structure conservation index 0.63
SVM decision value -0.03
SVM RNA-class probability 0.520564
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4184566 96 - 23771897
--A-UCCACAUCCAAGCGGACUACUAAGGGCGUCUUCGACACGACGCUGUUCAAGAGUCCCCUCAGCGAUAGGGAGAUGGAGAGAAAUCUCCAUGGGCU
--.-(((..((((.((.(((((...((.((((((........)))))).))....))))).))..).)))..))).(((((((....)))))))..... ( -35.10)
>DroVir_CAF1 33679 99 - 1
AAACCCGACGCCGAAGCGCACCACGAAAGGCGUCUUUGACACGACGCUCUUCAAGAGUCCCCUCAGCGAUCGGGAAAUGGAUCGUAAGCUCCAUUUGCU
...((((((((.............(((..(((((........)))))..)))..(((....))).))).)))))(((((((.(....).)))))))... ( -36.50)
>DroGri_CAF1 35465 99 - 1
AAAUCCGACACUGAAGCGCACCACCAAAGGCAUCUUCGAUACGACGCUCUUCAAAAGUCCCCAGAGCGAUCGGGAAAUGGAGCGCCAACUCCACGCCCU
...........(((((....((......))...)))))....((((((((............)))))).))(((...(((((......)))))..))). ( -24.30)
>DroSec_CAF1 30254 96 - 1
--A-CCCACAUCUAAGCGGACCACUAAGGGCGUCUUCGACACGACGCUGUUCAAGAGUCCCCUCAGCGAUCGGGAGAUGGAGAGAAAUCUCCAUGGGCU
--.-((((.((((....(((((...((.((((((........)))))).))...).))))(((........)))))))(((((....))))).)))).. ( -33.50)
>DroEre_CAF1 30699 96 - 1
--A-CCCACAUCCAAGCGAACCACUAAGGGCGUCUUCGACACGACGCUGUUCAAGAGUCCCCUCAGUGAUCGAGAAUUGGAGAGAAAUCUCCAUGGGGU
--.-((((........(((..((((.((((..((((.((((......)))).))))...)))).)))).))).....((((((....)))))))))).. ( -33.90)
>DroYak_CAF1 34738 96 - 1
--A-CCCACAUCCAAGCGAACCACCAAGGGCGUCUUCGAUACGACGCUGUUCAAGAGUCCCCUCAGUGAUCGAGAAAUGGAGAGAAAUCUCCAUGGGCU
--.-(((.........(((..(((.((.((((((........)))))).))...(((....))).))).)))....(((((((....)))))))))).. ( -31.10)
>consensus
__A_CCCACAUCCAAGCGAACCACUAAGGGCGUCUUCGACACGACGCUGUUCAAGAGUCCCCUCAGCGAUCGGGAAAUGGAGAGAAAUCUCCAUGGGCU
....((((..((...((........((.((((((........)))))).))...(((....))).))....))....((((((....)))))))))).. (-20.29 = -20.60 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:58 2006