Locus 968

Sequence ID	2R_DroMel_CAF1
Location	4,113,705 – 4,113,822
Length	117
Max. P	0.847314

overview

Window 2

Location	4,113,705 – 4,113,822
Length	117
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	91.60
Mean single sequence MFE	-28.68
Consensus MFE	-21.83
Energy contribution	-22.32
Covariance contribution	0.50
Combinations/Pair	1.14
Mean z-score	-2.48
Structure conservation index	0.76
SVM decision value	0.77
SVM RNA-class probability	0.847314
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4113705 117 + 20766785
CAUUGUUUUUUUUUUCCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU-UUUGUGGACAUGAAAAUGUCUGGGUCGUGGAAAA-AAAAACA
...(((((((((((((.....(((((.((((((((((..........((((........))))...(((.((((..-...))))))))))))).)).)).)))))))))))-))))))) ( -28.20)
>DroSim_CAF1 25254 117 + 1
CAUUGUUUUUUUU--UCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUUUUUUGUGGACAUGAAAAUGUCUGGGUCGGGGAAAAAAAAAACA
.....((((((((--(((....((((.((((((((((..........((((........))))...(((.((((......))))))))))))).)).)).)))).)))))))))))... ( -26.50)
>DroEre_CAF1 4444 110 + 1
CAUUGUUUU--UU--UCCGAAGCGACGCAGGUUUUCAGCUUUUUCUUCAGGUUUUCACUUCUGUUUUGUUCCACUU-UUUGUGGACAUGGAAAUGUCUGGGUCGG---AAGA-AAAACA
.....((((--((--((((((((((.(((((.....(((((.......)))))......))))).)))))((((..-...))((((((....)))))))).))))---))))-)))... ( -29.30)
>DroYak_CAF1 10917 113 + 1
CAUUGUUUUUUUU--UCCGAAGCGACGCAAUUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU-UUUGUGGACAUGAAAAUGUCUGGGUCGG---AAAAAAAAACA
...((((((((((--((((((((((.((((......(((((.......))))).......)))).)))))......-.....((((((....))))))...))))---))))))))))) ( -30.72)
>consensus
CAUUGUUUUUUUU__UCCGAAGCGACGCAACUUUUCAGCUUUUUCUUCAGGUUUUCACUUUUGUUUUGUUCCAUUU_UUUGUGGACAUGAAAAUGUCUGGGUCGG___AAAAAAAAACA
...((((((((((..(((((..(((((....((((((..........((((........))))...(((.((((......))))))))))))))))).)..)))))...)))))))))) (-21.83 = -22.32 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	4,113,705 – 4,113,822
Length	117
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	91.60
Mean single sequence MFE	-28.02
Consensus MFE	-19.94
Energy contribution	-21.25
Covariance contribution	1.31
Combinations/Pair	1.00
Mean z-score	-3.90
Structure conservation index	0.71
SVM decision value	0.35
SVM RNA-class probability	0.699138
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4113705 117 - 20766785
UGUUUUU-UUUUCCACGACCCAGACAUUUUCAUGUCCACAAA-AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGGAAAAAAAAAACAAUG
(((((((-((((((.(((....(((.((((((((((((....-...))).)))........((....)).))))))...((((....))))..)))...))))).)))))))))))... ( -27.80)
>DroSim_CAF1 25254 117 - 1
UGUUUUUUUUUUCCCCGACCCAGACAUUUUCAUGUCCACAAAAAAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGA--AAAAAAAACAAUG
(((((((((((((..((((.(((...(((((((.((((........))))...........))))))).))).......((((....))))..))))....)))--))))))))))... ( -26.30)
>DroEre_CAF1 4444 110 - 1
UGUUUU-UCUU---CCGACCCAGACAUUUCCAUGUCCACAAA-AAGUGGAACAAAACAGAAGUGAAAACCUGAAGAAAAAGCUGAAAACCUGCGUCGCUUCGGA--AA--AAAACAAUG
((((((-(.((---((((....(((.((((..(((((((...-..)))).)))...(((..((....)))))..))))..((.........)))))...)))))--))--))))))... ( -28.00)
>DroYak_CAF1 10917 113 - 1
UGUUUUUUUUU---CCGACCCAGACAUUUUCAUGUCCACAAA-AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAAUUGCGUCGCUUCGGA--AAAAAAAACAAUG
(((((((((((---((((....(((.((((((((((((....-...))).)))........((....)).))))))....((.........)))))...)))))--))))))))))... ( -30.00)
>consensus
UGUUUUUUUUU___CCGACCCAGACAUUUUCAUGUCCACAAA_AAAUGGAACAAAACAAAAGUGAAAACCUGAAGAAAAAGCUGAAAAGUUGCGUCGCUUCGGA__AAAAAAAACAAUG
((((((((((....((((....(((.((((((((((((........))).)))........((....)).))))))....((.........)))))...))))...))))))))))... (-19.94 = -21.25 +   1.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:59 2006