Locus 2660

Sequence ID 2L_DroMel_CAF1
Location 7,459,798 – 7,459,888
Length 90
Max. P 0.500000
window4236 window4237

overview

Window 6

Location 7,459,798 – 7,459,888
Length 90
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 79.46
Mean single sequence MFE -21.16
Consensus MFE -11.92
Energy contribution -14.54
Covariance contribution 2.62
Combinations/Pair 1.05
Mean z-score -1.90
Structure conservation index 0.56
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7459798 90 + 22407834
AAAAGCGAUGAUAGCGAAUCCCCCACUAGAAUCCA------AGUCACGCAUCCCCAGACGCGCUGUCUUCACUCGCUGCAGGUAAAUAUUUACCUG
...(((((.((((((((.((........)).))..------......((.((....)).)))))))).....))))).(((((((....))))))) ( -23.00)
>DroSec_CAF1 55906 89 + 1
AAAAGCGAUGAUAGCGAGUCCCCCACUAGAAUCCA------AGUCACGCAUC-CCAGACGCGCUGUCUCCACCUGCUGCAGGUAAUUAUUUACCUG
...((((..(((((((.(((...............------...........-...))).)))))))......)))).(((((((....))))))) ( -21.45)
>DroSim_CAF1 57448 89 + 1
AAAAGCGAUGAUAGCGAGUCCCCGACUACAAUCCA------AGUCACGCAUC-CCAGACGCGCUGUCUCCACCUGCUGCAGGUAAAUAUUUACCUG
...((((..(((((((.(((...((((........------))))..(....-.).))).)))))))......)))).(((((((....))))))) ( -24.40)
>DroYak_CAF1 57539 81 + 1
AAAAGCAAUUACAGUGAAUCUCCCACUGGAAUCCCCUUUCCCGUCACGC---------------AUCUCCACCAGCUGCAGGUAAAUAUUUACCUG
...(((.....(((((.......)))))(((......))).........---------------..........))).(((((((....))))))) ( -15.80)
>consensus
AAAAGCGAUGAUAGCGAAUCCCCCACUAGAAUCCA______AGUCACGCAUC_CCAGACGCGCUGUCUCCACCUGCUGCAGGUAAAUAUUUACCUG
...((((..(((((((.(((....................................))).)))))))......)))).(((((((....))))))) (-11.92 = -14.54 +   2.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 7,459,798 – 7,459,888
Length 90
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 79.46
Mean single sequence MFE -28.00
Consensus MFE -21.14
Energy contribution -21.57
Covariance contribution 0.44
Combinations/Pair 1.15
Mean z-score -1.43
Structure conservation index 0.75
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7459798 90 - 22407834
CAGGUAAAUAUUUACCUGCAGCGAGUGAAGACAGCGCGUCUGGGGAUGCGUGACU------UGGAUUCUAGUGGGGGAUUCGCUAUCAUCGCUUUU
(((((((....)))))))....((((((.((.((((((((....)))))......------.(((((((.....)))))))))).)).)))))).. ( -31.40)
>DroSec_CAF1 55906 89 - 1
CAGGUAAAUAAUUACCUGCAGCAGGUGGAGACAGCGCGUCUGG-GAUGCGUGACU------UGGAUUCUAGUGGGGGACUCGCUAUCAUCGCUUUU
(((((((....)))))))...((((((....).(((((((...-))))))).)))------))(((..((((((....).)))))..)))...... ( -30.60)
>DroSim_CAF1 57448 89 - 1
CAGGUAAAUAUUUACCUGCAGCAGGUGGAGACAGCGCGUCUGG-GAUGCGUGACU------UGGAUUGUAGUCGGGGACUCGCUAUCAUCGCUUUU
(((((((....)))))))...((((((....).(((((((...-))))))).)))------))(((.(((((.(....)..))))).)))...... ( -29.20)
>DroYak_CAF1 57539 81 - 1
CAGGUAAAUAUUUACCUGCAGCUGGUGGAGAU---------------GCGUGACGGGAAAGGGGAUUCCAGUGGGAGAUUCACUGUAAUUGCUUUU
((.(((....((((((.......))))))..)---------------)).)).....(((((.((((.((((((.....)))))).)))).))))) ( -20.80)
>consensus
CAGGUAAAUAUUUACCUGCAGCAGGUGGAGACAGCGCGUCUGG_GAUGCGUGACU______UGGAUUCUAGUGGGGGACUCGCUAUCAUCGCUUUU
(((((((....))))))).(((...........(((((((....)))))))............(((..(((((((...)))))))..))))))... (-21.14 = -21.57 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:06 2006