Locus 4300

Sequence ID	2R_DroMel_CAF1
Location	14,138,743 – 14,138,854
Length	111
Max. P	0.943721

overview

Window 9

Location	14,138,743 – 14,138,854
Length	111
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	76.40
Mean single sequence MFE	-22.08
Consensus MFE	-11.78
Energy contribution	-12.45
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.53
SVM decision value	1.34
SVM RNA-class probability	0.943721
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14138743 111 + 20766785
UUCUUAUCAUUUAAGU--CUAUAGCUAUUAACUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCACACCAUUCUUGGCCCCAUUUUGCCAUUUUUAUUUAGCUCCCAGCCCAC
...........(((((--..((....))..)))))...((((((.....(((((.....)).))).........((((........))))..............))))))... ( -19.40)
>DroPse_CAF1 11967 101 + 1
----------UAAAGC--CUACAAUUGGCAGCUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCAAACCAUUCGCGGACCCAUUUUCCCGUUUUUGUUCAAUUCCCAGCCAAC
----------....((--(.......))).......((((((((.....(((((.....)).)))...((...((((..........))))...))........)))))))). ( -24.70)
>DroEre_CAF1 8686 111 + 1
UUCUUAUCAUUUGUGU--CUAUAGCUAUUAUCUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCUGACCAUUCUUGGGCCCAUUUUGCCAUUUUUAUUUAGCUCCCAACCCAC
...........((.((--....(((((..........(((((((..(((....(((.........)))......)))..)))....))))........)))))....)).)). ( -17.67)
>DroYak_CAF1 8670 99 + 1
UUCUUAUCAAU--------------AAUUAUCUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCAGACCAUUCUCGGUCCCAUUUUGCCAUUUUUAUUUAGCUCCCAGCCCAC
...........--------------.............((((((.....(((((.....)).)))((((......)))).........................))))))... ( -19.20)
>DroAna_CAF1 8878 113 + 1
UGGCUAUCAAUUAAGUAGCUUGAGCGAAGAGCUUACUUUGCCGGAUCCAUGCUGUCCCUCAUGCAGACCAUUCUGGGACCCAUUUUUCCAUUCUUAUUUGCCUCCCAGCCCAC
.((((..(((.((((......(.((((((......)))))))(((...(((..(((((..(((.....)))...))))).)))...)))...)))).)))......))))... ( -26.00)
>DroPer_CAF1 8643 101 + 1
----------UAAUGC--CUACAAUUGGCAGCUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCAAACCAUUCGCGGACCCAUUUUCCCGUUUUUGUUCAAUUCCCAGCCAAC
----------...(((--(.......))))......((((((((.....(((((.....)).)))...((...((((..........))))...))........)))))))). ( -25.50)
>consensus
UUCUUAUCA_UUAAGU__CUACAGCUAUUAGCUUACUUGGCUGGAUCCAUGCUGUCCCUCAUGCAGACCAUUCUCGGACCCAUUUUGCCAUUUUUAUUUAGCUCCCAGCCCAC
......................................((((((.....(((((.....)).)))..((......))...........................))))))... (-11.78 = -12.45 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	14,138,743 – 14,138,854
Length	111
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	76.40
Mean single sequence MFE	-26.59
Consensus MFE	-16.43
Energy contribution	-16.27
Covariance contribution	-0.17
Combinations/Pair	1.40
Mean z-score	-1.61
Structure conservation index	0.62
SVM decision value	0.66
SVM RNA-class probability	0.814592
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14138743 111 - 20766785
GUGGGCUGGGAGCUAAAUAAAAAUGGCAAAAUGGGGCCAAGAAUGGUGUGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGUUAAUAGCUAUAG--ACUUAAAUGAUAAGAA
...(((((((.............((((........))))...(((.(((.(.....).))).)))...)))))))...((((((.((....)).)--)))))........... ( -27.00)
>DroPse_CAF1 11967 101 - 1
GUUGGCUGGGAAUUGAACAAAAACGGGAAAAUGGGUCCGCGAAUGGUUUGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGCUGCCAAUUGUAG--GCUUUA----------
.(((((((((....((((.....(((((.......))).))....)))).((((........))))..)))))))))..(((((..(....)..)--))))..---------- ( -26.30)
>DroEre_CAF1 8686 111 - 1
GUGGGUUGGGAGCUAAAUAAAAAUGGCAAAAUGGGCCCAAGAAUGGUCAGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGAUAAUAGCUAUAG--ACACAAAUGAUAAGAA
(((..(((..(((((........((((....(((..(((.(....(((..(....).)))..).)))..)))))))..........))))).)))--.)))............ ( -22.77)
>DroYak_CAF1 8670 99 - 1
GUGGGCUGGGAGCUAAAUAAAAAUGGCAAAAUGGGACCGAGAAUGGUCUGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGAUAAUU--------------AUUGAUAAGAA
...(((((((.((((........))))......(((((......))))).((((........))))..))))))).(((((.....))--------------)))........ ( -25.10)
>DroAna_CAF1 8878 113 - 1
GUGGGCUGGGAGGCAAAUAAGAAUGGAAAAAUGGGUCCCAGAAUGGUCUGCAUGAGGGACAGCAUGGAUCCGGCAAAGUAAGCUCUUCGCUCAAGCUACUUAAUUGAUAGCCA
.(((((..((((.(.........((((...(((.(((((...(((.....)))..)))))..)))...)))).........)))))..))))).(((((......).)))).. ( -31.07)
>DroPer_CAF1 8643 101 - 1
GUUGGCUGGGAAUUGAACAAAAACGGGAAAAUGGGUCCGCGAAUGGUUUGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGCUGCCAAUUGUAG--GCAUUA----------
.(((((((((....((((.....(((((.......))).))....)))).((((........))))..)))))))))......((((.......)--)))...---------- ( -27.30)
>consensus
GUGGGCUGGGAGCUAAAUAAAAAUGGCAAAAUGGGUCCGAGAAUGGUCUGCAUGAGGGACAGCAUGGAUCCAGCCAAGUAAGCUAAUAGCUAUAG__ACUUAA_UGAUAAGAA
...(((((((.............((((........))))...........((((........))))..)))))))...................................... (-16.43 = -16.27 +  -0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:31 2006