Locus 7402

Sequence ID 3R_DroMel_CAF1
Location 19,660,928 – 19,661,039
Length 111
Max. P 0.999832
window11963 window11964

overview

Window 3

Location 19,660,928 – 19,661,039
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.42
Mean single sequence MFE -31.16
Consensus MFE -13.41
Energy contribution -15.01
Covariance contribution 1.60
Combinations/Pair 1.15
Mean z-score -3.31
Structure conservation index 0.43
SVM decision value 4.03
SVM RNA-class probability 0.999763
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19660928 111 + 27905053
-CCCCGCAAGUGAAAUGAGAUGCAGUAAGUGCAGUAAUGGAU--AUGUAAUCAUCA-CAAAAUCCAAAU-----GAUUACAAAAGCCAUCGCGCUGCACUUGGGUAAGCCAACGAAGGGA
-.((((((............)))..((((((((((.((((..--.(((((((((..-..........))-----)))))))....))))...))))))))))((....))......))). ( -33.30)
>DroSec_CAF1 45017 109 + 1
-UCCCGCAAGUGAAAUGAGAUGCAGUAAGUGCAGUAAUGGAU--AUGUAAUCAUUG-CAAAAUCCACAU-----GAUUACAAAAGCCAUCG--CUGCACUUGGCUAAGCCAACGAAGGGA
-(((((((............))).((((((((((..((((..--.(((((((((((-.......)).))-----)))))))....))))..--))))))))(((...))).))...)))) ( -37.80)
>DroSim_CAF1 45237 109 + 1
-CCCCGCAAGUGAAAUGAGAUGCAGUAAGUGCAGUAAUGGAU--AUGUAAUCAUCG-CAAAAUCCACAU-----GAUUACAAAAGCCAUCG--CUGCACUUGGGUAAGCCAACGAAGGGA
-.((((((............)))..(((((((((..((((..--.(((((((((..-..........))-----)))))))....))))..--)))))))))((....))......))). ( -36.30)
>DroYak_CAF1 45733 112 + 1
CUGCUGCAAGUGAAAUGAGAUGCAGUAAGUGCAGUAAUGGAUAUAUGUAAUCAUCGACAAAAUCCACAU-----GAUUACAAAAGCCAUCG--CUGCACUCAAGUAAGCCAACUGAG-GA
.(((((((............)))))))(((((((..((((.....(((((((((.((.....))...))-----)))))))....))))..--)))))))........((......)-). ( -34.00)
>DroAna_CAF1 49044 100 + 1
-----AGAACUCAAAUGAGAUGCAGUAACUG-ACUAA--GAUGAAUGUAUUC-----CAAUAUUCAAACUCUACGAAGGCAGAGGCCAAAC--AUACACACUAUUAAAAUCAUUG-----
-----.((.(((....))).....(((....-.....--..(((((((....-----..)))))))..((((.(....).)))).......--.)))............))....----- ( -14.40)
>consensus
_CCCCGCAAGUGAAAUGAGAUGCAGUAAGUGCAGUAAUGGAU__AUGUAAUCAUCG_CAAAAUCCACAU_____GAUUACAAAAGCCAUCG__CUGCACUUGGGUAAGCCAACGAAGGGA
.........................(((((((((..((((.....(((((((......................)))))))....))))....))))))))).................. (-13.41 = -15.01 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 19,660,928 – 19,661,039
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.42
Mean single sequence MFE -33.02
Consensus MFE -16.51
Energy contribution -17.75
Covariance contribution 1.24
Combinations/Pair 1.20
Mean z-score -3.41
Structure conservation index 0.50
SVM decision value 4.19
SVM RNA-class probability 0.999832
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19660928 111 - 27905053
UCCCUUCGUUGGCUUACCCAAGUGCAGCGCGAUGGCUUUUGUAAUC-----AUUUGGAUUUUG-UGAUGAUUACAU--AUCCAUUACUGCACUUACUGCAUCUCAUUUCACUUGCGGGG-
..((......))....(((((((((((...(((((....(((((((-----(((.........-.)))))))))).--..))))).))))))))...(((............)))))).- ( -33.90)
>DroSec_CAF1 45017 109 - 1
UCCCUUCGUUGGCUUAGCCAAGUGCAG--CGAUGGCUUUUGUAAUC-----AUGUGGAUUUUG-CAAUGAUUACAU--AUCCAUUACUGCACUUACUGCAUCUCAUUUCACUUGCGGGA-
((((......(((...)))((((((((--..((((....(((((((-----(((..(...)..-).))))))))).--..))))..))))))))...(((............)))))))- ( -38.60)
>DroSim_CAF1 45237 109 - 1
UCCCUUCGUUGGCUUACCCAAGUGCAG--CGAUGGCUUUUGUAAUC-----AUGUGGAUUUUG-CGAUGAUUACAU--AUCCAUUACUGCACUUACUGCAUCUCAUUUCACUUGCGGGG-
..((......))....(((((((((((--..((((....(((((((-----(((..(...)..-).))))))))).--..))))..))))))))...(((............)))))).- ( -37.30)
>DroYak_CAF1 45733 112 - 1
UC-CUCAGUUGGCUUACUUGAGUGCAG--CGAUGGCUUUUGUAAUC-----AUGUGGAUUUUGUCGAUGAUUACAUAUAUCCAUUACUGCACUUACUGCAUCUCAUUUCACUUGCAGCAG
.(-(......))......(((((((((--..((((....(((((((-----((.(((......)))))))))))).....))))..)))))))))(((((............)))))... ( -34.90)
>DroAna_CAF1 49044 100 - 1
-----CAAUGAUUUUAAUAGUGUGUAU--GUUUGGCCUCUGCCUUCGUAGAGUUUGAAUAUUG-----GAAUACAUUCAUC--UUAGU-CAGUUACUGCAUCUCAUUUGAGUUCU-----
-----...(((((.....(((((((((--(((..(.((((((....)))))).)..)))))..-----..)))))))....--..)))-))..........(((....)))....----- ( -20.40)
>consensus
UCCCUUCGUUGGCUUACCCAAGUGCAG__CGAUGGCUUUUGUAAUC_____AUGUGGAUUUUG_CGAUGAUUACAU__AUCCAUUACUGCACUUACUGCAUCUCAUUUCACUUGCGGGA_
...................((((((((...(((((....(((((((......................))))))).....))))).)))))))).(((((............)))))... (-16.51 = -17.75 +   1.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:02 2006