Locus 3842

Sequence ID	2R_DroMel_CAF1
Location	12,688,113 – 12,688,210
Length	97
Max. P	0.740514

overview

Window 5

Location	12,688,113 – 12,688,210
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.25
Mean single sequence MFE	-28.52
Consensus MFE	-22.66
Energy contribution	-22.27
Covariance contribution	-0.39
Combinations/Pair	1.11
Mean z-score	-1.87
Structure conservation index	0.79
SVM decision value	0.45
SVM RNA-class probability	0.740514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12688113 97 + 20766785
------------------GGG---AAA--CCUCGCCAUGCAGCAUUUAUUGCCAGCGAAGCGUAUUUGGCACAUUUGAUGCGGCGCAUAAUGGGGAACGCCAUUAAAUGUCCAUUGACAU
------------------((.---...--))..((..(((.(((.....)))..)))..))((...(((.((((((((((((.(.(.....).)...)).)))))))))))))...)).. ( -29.10)
>DroVir_CAF1 60853 91 + 1
-----------------------------CCUCGCCAUGCAGCAUUUAUUGCCAACGAAGCGUAUUUGGUGCAUUUGAUGCGCUGCAUAAUGGCGCACGCCAUUAAAUGUCCAUUGACAU
-----------------------------........((((((.......(((((((...)))...))))((((...))))))))))(((((((....))))))).(((((....))))) ( -27.90)
>DroGri_CAF1 46478 117 + 1
UAAAGGCAAAAAUAGAAAGGA---AAAACUCUAGCCAUGCAGCAUUUAUUGCCAACGAAGCGUAUUUGGUGCAUUUGAUGCGCUGCAUAAUGGCGCACGCCAUUAAAUGUCCAUUGACAU
....(((.....((((.....---.....))))))).((((((.......(((((((...)))...))))((((...))))))))))(((((((....))))))).(((((....))))) ( -31.80)
>DroEre_CAF1 41870 97 + 1
------------------GGG---AGA--ACUCGCCAUGCAGCAUUUAUUGCCAGCGAAGCGUAUUUGGCACAUUUGAUGCGGCGCAUAAUGGGGAACGCCAUUAAAUGUCCAUUGACAU
------------------(((---...--.)))((..(((.(((.....)))..)))..))((...(((.((((((((((((.(.(.....).)...)).)))))))))))))...)).. ( -25.60)
>DroWil_CAF1 54819 100 + 1
------------------GUGAAAAAA--CCUCACCAUGCAGCAUUUAUUGCCAACGAAGCGUAUUUGGCACAUUUGAUGCGGCGCAUAAUGGCAAACGCCAUUAAAUGUCCAUUGACAU
------------------((((.....--..))))...((.(((((...((((((((...)))...))))).....))))).))...(((((((....))))))).(((((....))))) ( -27.70)
>DroMoj_CAF1 89883 91 + 1
-----------------------------CGUCGCCAUGCAGCAUUUAUUGCCAACGAAGCGUAUUUGGUGCAUUUGAUGCGCUGCAUAAUGGCGCACGCCAUUAAAUGUCCAUUGACAU
-----------------------------((((((((((((((.......(((((((...)))...))))((((...))))))))))...))))).))).......(((((....))))) ( -29.00)
>consensus
__________________GGG___AAA__CCUCGCCAUGCAGCAUUUAUUGCCAACGAAGCGUAUUUGGCACAUUUGAUGCGCCGCAUAAUGGCGAACGCCAUUAAAUGUCCAUUGACAU
.....................................(((.(((((...((((((((...)))...))))).....)))))...)))(((((((....))))))).(((((....))))) (-22.66 = -22.27 +  -0.39)

alignment

secondary structure

dotplot

Window 6

Location	12,688,113 – 12,688,210
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.25
Mean single sequence MFE	-28.53
Consensus MFE	-19.95
Energy contribution	-20.23
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.70
SVM decision value	0.10
SVM RNA-class probability	0.584577
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12688113 97 - 20766785
AUGUCAAUGGACAUUUAAUGGCGUUCCCCAUUAUGCGCCGCAUCAAAUGUGCCAAAUACGCUUCGCUGGCAAUAAAUGCUGCAUGGCGAGG--UUU---CCC------------------
.......(((((((((..((((((..........))))))....)))))).))).....((((((((((((........))).))))))))--)..---...------------------ ( -28.50)
>DroVir_CAF1 60853 91 - 1
AUGUCAAUGGACAUUUAAUGGCGUGCGCCAUUAUGCAGCGCAUCAAAUGCACCAAAUACGCUUCGUUGGCAAUAAAUGCUGCAUGGCGAGG-----------------------------
.(((((.........(((((((....)))))))((((((((((...)))).........(((.....))).......)))))))))))...----------------------------- ( -28.60)
>DroGri_CAF1 46478 117 - 1
AUGUCAAUGGACAUUUAAUGGCGUGCGCCAUUAUGCAGCGCAUCAAAUGCACCAAAUACGCUUCGUUGGCAAUAAAUGCUGCAUGGCUAGAGUUUU---UCCUUUCUAUUUUUGCCUUUA
(((((....))))).(((((((....)))))))((((((((((...)))).........(((.....))).......)))))).((((((((....---....))))).....))).... ( -33.00)
>DroEre_CAF1 41870 97 - 1
AUGUCAAUGGACAUUUAAUGGCGUUCCCCAUUAUGCGCCGCAUCAAAUGUGCCAAAUACGCUUCGCUGGCAAUAAAUGCUGCAUGGCGAGU--UCU---CCC------------------
.......(((((((((..((((((..........))))))....)))))).)))....((((..((.((((.....))))))..))))...--...---...------------------ ( -26.00)
>DroWil_CAF1 54819 100 - 1
AUGUCAAUGGACAUUUAAUGGCGUUUGCCAUUAUGCGCCGCAUCAAAUGUGCCAAAUACGCUUCGUUGGCAAUAAAUGCUGCAUGGUGAGG--UUUUUUCAC------------------
(((((....))))).(((((((....)))))))...((.((((......((((((..........))))))....)))).))...(((((.--....)))))------------------ ( -26.20)
>DroMoj_CAF1 89883 91 - 1
AUGUCAAUGGACAUUUAAUGGCGUGCGCCAUUAUGCAGCGCAUCAAAUGCACCAAAUACGCUUCGUUGGCAAUAAAUGCUGCAUGGCGACG-----------------------------
(((((....))))).......(((.(((((...((((((((((...)))).........(((.....))).......))))))))))))))----------------------------- ( -28.90)
>consensus
AUGUCAAUGGACAUUUAAUGGCGUGCGCCAUUAUGCACCGCAUCAAAUGCACCAAAUACGCUUCGUUGGCAAUAAAUGCUGCAUGGCGAGG__UUU___CCC__________________
.(((((((((((...(((((((....)))))))......((((...)))).........).))))))))))......(((....)))................................. (-19.95 = -20.23 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:20 2006