Locus 8135

Sequence ID	3L_DroMel_CAF1
Location	21,444,892 – 21,444,986
Length	94
Max. P	0.935003

overview

Window 0

Location	21,444,892 – 21,444,986
Length	94
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.32
Mean single sequence MFE	-21.57
Consensus MFE	-15.65
Energy contribution	-15.73
Covariance contribution	0.08
Combinations/Pair	1.20
Mean z-score	-1.71
Structure conservation index	0.73
SVM decision value	1.24
SVM RNA-class probability	0.935003
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21444892 94 + 23771897
AAAGUUUAUUGAUAUUAUUUUUCCUAAAA-A------------UGUUUUUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
..................(((((((((((-.------------...))))))))))).(((((((........))))(((((.....))))).........)))... ( -22.00)
>DroSec_CAF1 3540 105 + 1
AAAGUUUAUUGAAAACAUAUUUCCUAAAA-U-GUGCCACAUUUUGUUUUUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
...(.(((((..............(((((-(-(.....)))))))....((((.(((((((((((........))))).)))))))))).........))))).).. ( -21.80)
>DroSim_CAF1 1005 105 + 1
AAAGUUUAUUGAAAACAUAUUUUCUAAAA-U-GUGCCACAUUUUGUUUUUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
...(.((((((((((....)))))(((((-(-(.....)))))))....((((.(((((((((((........))))).)))))))))).........))))).).. ( -22.20)
>DroEre_CAF1 3593 101 + 1
AAACUU-UUUAAAAAUAUUUUUCCUCAAA-U-GUAACUCAUU---UUUGUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
......-...................(((-(-(.....))))---)..(((((.(((((((((((........))))).)))))))))))................. ( -22.00)
>DroYak_CAF1 1127 101 + 1
AAAGUU-AUUGAUAAACUUCUUCCUAAAA-U-GUAACUCGUU---UCUUUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
...(((-(((...........((((((((-(-(.....))).---..)))))))(((((((((((........))))).)))))).............))))))... ( -21.60)
>DroMoj_CAF1 2733 88 + 1
----UUUAUUGUGAAUUAAUU--CUA--AUUUU-----------AAUUUUAGCGGACUGUUGCCAAUCAUGUAUGGCACGCAUACCCUAUGCAACGCUAAUAGCAAC
----....(((((((((((..--...--...))-----------)))))(((((......(((((........))))).(((((...)))))..)))))...)))). ( -19.80)
>consensus
AAAGUUUAUUGAAAAUAUAUUUCCUAAAA_U_GU__C_CAUU__GUUUUUAGGAGAAUGCUGCCAAUCCUGCAUGGCGCGUAUUCCCUACGCCACCCUGAUAGCCAC
.................................................((((.(((((((((((........))))).)))))))))).................. (-15.65 = -15.73 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	21,444,892 – 21,444,986
Length	94
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.32
Mean single sequence MFE	-24.33
Consensus MFE	-17.45
Energy contribution	-18.10
Covariance contribution	0.64
Combinations/Pair	1.16
Mean z-score	-1.18
Structure conservation index	0.72
SVM decision value	0.45
SVM RNA-class probability	0.739950
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21444892 94 - 23771897
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUAAAAACA------------U-UUUUAGGAAAAAUAAUAUCAAUAAACUUU
((.((((((.(.(((((((.(......)))))))).)..)).)))).))....((((((((...------------.-))))))))..................... ( -25.30)
>DroSec_CAF1 3540 105 - 1
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUAAAAACAAAAUGUGGCAC-A-UUUUAGGAAAUAUGUUUUCAAUAAACUUU
((((((((....)))(((((.....))))))))))..((.(((((.(((((..((((((((..............-.-))))))))...))))).)))))...)).. ( -25.86)
>DroSim_CAF1 1005 105 - 1
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUAAAAACAAAAUGUGGCAC-A-UUUUAGAAAAUAUGUUUUCAAUAAACUUU
(((((((.((...((...((((((((..((((((........)))).)))))).))))....))...)))))).)-)-)....(((((....))))).......... ( -24.90)
>DroEre_CAF1 3593 101 - 1
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUACAAA---AAUGAGUUAC-A-UUUGAGGAAAAAUAUUUUUAAA-AAGUUU
((((((((....)))))(((((((((..((((((........)))).)))))).)))))...---.......)))-.-((((((((......))))))))-...... ( -26.30)
>DroYak_CAF1 1127 101 - 1
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUAAAGA---AACGAGUUAC-A-UUUUAGGAAGAAGUUUAUCAAU-AACUUU
((.((((((.(.(((((((.(......)))))))).)..)).)))).))....((((((((.---..........-.-)))))))).((((((.......-)))))) ( -25.50)
>DroMoj_CAF1 2733 88 - 1
GUUGCUAUUAGCGUUGCAUAGGGUAUGCGUGCCAUACAUGAUUGGCAACAGUCCGCUAAAAUU-----------AAAAU--UAG--AAUUAAUUCACAAUAAA----
((((...((((((..(((((...))))).(((((........)))))......))))))....-----------.....--..(--((....))).))))...---- ( -18.10)
>consensus
GUGGCUAUCAGGGUGGCGUAGGGAAUACGCGCCAUGCAGGAUUGGCAGCAUUCUCCUAAAAAC__AAUG_G__AC_A_UUUUAGGAAAAAUAUUUUCAAUAAACUUU
((.((((((.(.(((((((.(......)))))))).)..)).)))).))....((((((((.................))))))))..................... (-17.45 = -18.10 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:10 2006