Locus 7932

Sequence ID	3R_DroMel_CAF1
Location	21,259,586 – 21,259,843
Length	257
Max. P	0.952423

overview

Window 9

Location	21,259,586 – 21,259,692
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.11
Mean single sequence MFE	-22.45
Consensus MFE	-13.00
Energy contribution	-12.81
Covariance contribution	-0.19
Combinations/Pair	1.25
Mean z-score	-1.62
Structure conservation index	0.58
SVM decision value	0.07
SVM RNA-class probability	0.566798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21259586 106 - 27905053
AAGGUAUCCAAGCUUUAGAUAGCUUGAAUAUUAUUUGG-GAAAAAGUUCACGAGUUGCUUUUUAGCAAAUGAUUCUAUUCUAGAAGGUGAUUUAAGUAAAGAUACAU-------------
...(((((((((((......))))))....((((((..-(((....)))..((((..((((((((..((((....))))))))))))..)))))))))).)))))..------------- ( -24.90)
>DroSec_CAF1 84454 94 - 1
AAGGUAUCCAAACU----------UAUAUUUUAUUUGG-GAUAAAGUUCACGAGUUGCUGUUUAGAUGUUGAUUU--UUCUAGAAGGUGACUUAAGUAAAGAUACAU-------------
...(((((...(((----------(..((((((((...-))))))))....((((..((.((((((.........--.)))))).))..))))))))...)))))..------------- ( -20.80)
>DroSim_CAF1 87178 94 - 1
AAGGUAUCCAAACU----------UAUAUUUUAUAUGG-GAUAAAGGUCACGAGUUGCUGUUUAGCUAUUGAUUU--UUCUAGAAGGUGACUUAAGUAAAGAUACAU-------------
...(((((...(((----------(..........(((-((...((((((..(((((.....)))))..))))))--))))).(((....)))))))...)))))..------------- ( -18.10)
>DroYak_CAF1 93975 118 - 1
AAUGUAUCCACAAUUUAAAUAACUUGUGAUUUAUUUGGGGAUAACGUCCGUGAGUGGCUUUUUAGUUAUUGAUAU--UUUUAGAAGGUGACUUAAGUAAAGUUGCAUUUAUUUAAACGAC
.............(((((((((..((..((((......((((...)))).(((((.(((((((((..((....))--..))))))))).)))))....))))..)).))))))))).... ( -26.00)
>consensus
AAGGUAUCCAAACU__________UAUAUUUUAUUUGG_GAUAAAGUUCACGAGUUGCUGUUUAGCUAUUGAUUU__UUCUAGAAGGUGACUUAAGUAAAGAUACAU_____________
...(((((...........................(((.........))).((((..((((((((..............))))))))..)))).......)))))............... (-13.00 = -12.81 +  -0.19)

alignment

secondary structure

dotplot

Window 0

Location	21,259,692 – 21,259,804
Length	112
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	95.72
Mean single sequence MFE	-28.57
Consensus MFE	-24.73
Energy contribution	-25.23
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.87
SVM decision value	0.13
SVM RNA-class probability	0.599929
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21259692 112 - 27905053
GUUUUUUUAUCCGACAUCAUGUGCAUGAUGUUAAUGCGCUAAGUGCAAUGCGAAACAAGGGGA-AAACCCAAAUGAUUUAUGGCAAGCGGAUCACGUGAGCCAAAUUUUU-AUA
(((((.......((((((((....))))))))..(((((...)))))....)))))..(((..-...)))..........((((..(((.....)))..)))).......-... ( -30.40)
>DroSec_CAF1 84548 113 - 1
GUUU-UUUAUCCGACAUCAUGUGCAUGAUGUUAAUGCGCUAAGUGCAAUGCGAAACAAGGGAACAAACCCAAAUGAUUUAUGGCAAGCGGAUCACGUGAGCCAAAUUUUUGAUA
((((-(.(((..((((((((....))))))))..(((((...)))))))).)))))..(((......)))..........((((..(((.....)))..))))........... ( -29.70)
>DroSim_CAF1 87272 112 - 1
GUUU-UUUAUCCGACAUCAUGUGCAUGAUGUUAAUGCGCUAAGUGCAAUGCGAAACAAGGGGA-AAACCCAAAUGAUUUAUGGCAAGCGAAUCACGUGAGCCAAAUUUUUGAUA
((((-(.(((..((((((((....))))))))..(((((...)))))))).)))))..(((..-...)))..........((((..(((.....)))..))))........... ( -29.50)
>DroYak_CAF1 94093 111 - 1
GUUU-UUUAUCCGACAUCAUGUGCAUGAUGUUAAUGCGCUAAGUGCAAUGCGAAACAAGUGAA-AAACCCAAAUGAUUUAUGGCAAGGGGGUCACGUAAGCCAAAUUUUU-AUA
((((-(.(((..((((((((....))))))))..(((((...)))))))).)))))..((((.-...(((...((........))..))).))))...............-... ( -24.70)
>consensus
GUUU_UUUAUCCGACAUCAUGUGCAUGAUGUUAAUGCGCUAAGUGCAAUGCGAAACAAGGGAA_AAACCCAAAUGAUUUAUGGCAAGCGGAUCACGUGAGCCAAAUUUUU_AUA
((((........((((((((....))))))))..(((((...))))).....))))..(((......)))..........((((..(((.....)))..))))........... (-24.73 = -25.23 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	21,259,731 – 21,259,843
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.20
Mean single sequence MFE	-32.36
Consensus MFE	-10.48
Energy contribution	-14.00
Covariance contribution	3.52
Combinations/Pair	1.14
Mean z-score	-2.23
Structure conservation index	0.32
SVM decision value	1.42
SVM RNA-class probability	0.952423
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21259731 112 - 27905053
CAUCAUUGUUUGGUUACUUCUCUGGGUUU-UUGUGUCCACGUUUUUUUAUCCGACAUCAUGUGCAUG--AU--GUUAAUGCGCUAAGUGCAAUGCGA--AACAAGGGGA-AAACCCAAAU
.......((((((....((((((..((((-(.((((................((((((((....)))--))--)))..(((((...)))))))))))--)))..)))))-)...)))))) ( -28.40)
>DroSec_CAF1 84588 111 - 1
CAUCAUUGUUGGGUUACUUUUCUGGGUU--UUGCGUCCACGUUU-UUUAUCCGACAUCAUGUGCAUG--AU--GUUAAUGCGCUAAGUGCAAUGCGA--AACAAGGGAACAAACCCAAAU
........(((((((..((..((..(((--((((((........-.......((((((((....)))--))--)))..(((((...)))))))))))--))).))..))..))))))).. ( -36.30)
>DroSim_CAF1 87312 110 - 1
CAUCAUUGUUGGGUUACUUUUCUGGGUU--UUGCGUCCACGUUU-UUUAUCCGACAUCAUGUGCAUG--AU--GUUAAUGCGCUAAGUGCAAUGCGA--AACAAGGGGA-AAACCCAAAU
........(((((((..((..((..(((--((((((........-.......((((((((....)))--))--)))..(((((...)))))))))))--)))..))..)-)))))))).. ( -36.80)
>DroYak_CAF1 94132 110 - 1
CAUCAUUGUUGAGUUACUUUUCUGGGUU--UUGGGUUCACGUUU-UUUAUCCGACAUCAUGUGCAUG--AU--GUUAAUGCGCUAAGUGCAAUGCGA--AACAAGUGAA-AAACCCAAAU
..(((....)))..........((((((--((....((((((((-(.(((..((((((((....)))--))--)))..(((((...)))))))).))--)))..)))))-)))))))... ( -27.60)
>DroAna_CAF1 78420 98 - 1
CAGCUCUGA----GGACUUUUCGGGAUCCGUUGGGU----GUCU-UUAAUG------------CAGGGGAUCCACUAAUGUGCCGAGUGCACUGGGAUAAAUCAGGGCC-AAGUAAGCAU
..(((((((----.....(..((((((((.(((.((----....-...)).------------))).))))))......((((.....))))))..)....))))))).-.......... ( -32.70)
>consensus
CAUCAUUGUUGGGUUACUUUUCUGGGUU__UUGCGUCCACGUUU_UUUAUCCGACAUCAUGUGCAUG__AU__GUUAAUGCGCUAAGUGCAAUGCGA__AACAAGGGAA_AAACCCAAAU
........(((((((...(((((..(((.(((((((..........................((((...........))))((.....)).))))))).)))..)))))..))))))).. (-10.48 = -14.00 +   3.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:27 2006