Locus 2372

Sequence ID	2L_DroMel_CAF1
Location	6,445,262 – 6,445,369
Length	107
Max. P	0.854459

overview

Window 3

Location	6,445,262 – 6,445,369
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.51
Mean single sequence MFE	-30.15
Consensus MFE	-15.38
Energy contribution	-15.02
Covariance contribution	-0.36
Combinations/Pair	1.22
Mean z-score	-1.64
Structure conservation index	0.51
SVM decision value	0.03
SVM RNA-class probability	0.551190
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6445262 107 + 22407834
AG--UUGCUUAUGGUA-GA-CCACUUACGUUUCCAUCGCUCAUGCCCAGAGGAGAGUUUAGAAUAAAGUCUGUGGGAGCAAUGGCAUCCACCAGAGCAAUGGCUUCGUUCU
..--.......(((..-..-)))...(((...((((.((((.(((((...(.(((.((((...)))).))).).)).))).(((......))))))).))))...)))... ( -27.30)
>DroVir_CAF1 28898 108 + 1
CA--AAAAAAAAAGCGCAG-CUACAUACAUUGCCAUCACUCAUGCCCAGCGGAGAAUUGAGAAUGAAAUCCGUGGGUGCGAUAGCAUCCACCAGAGCAAUCGCUUCGUUCU
..--.......(((((..(-((.....((((..((...(((.(((...))))))...))..))))......((((((((....))))))))...)))...)))))...... ( -28.10)
>DroGri_CAF1 26130 108 + 1
AA--AUGCUUAAAUAACAG-UUACUCACAUUGCCAUCACUCAUGCCCAGCGGCGAGUUCAAAACGAAAUCGGUGGGUGCAAUUGCAUCCACCAAGGCAAUGGCUUCAUUCU
..--...............-.......(((((((...((((..(((....))))))).............(((((((((....)))))))))..))))))).......... ( -35.30)
>DroYak_CAF1 14267 107 + 1
GG--UUGCUUUUAGUA-GA-UCACUUACGUUUCCAUCGCUCAUGCCCAGAGGAGAGUUUAGAAUAAAGUCUGUGGGAGCAAUGGCAUCCACCAGAGCAAUAGCUUCGUUCU
((--.((((....(((-(.-....))))((((((((..(((.......))).(((.((((...)))).)))))))))))...)))).))..(..(((....)))..).... ( -24.30)
>DroMoj_CAF1 38598 104 + 1
AA--A----UAUUUUAUAA-CUGCUUACAUUGCCAUCGCUCAUGCCCAAUGGCGAGUUCAAAAUGAAAUCUGUGGGCGCAAUUGCAUCCACCAGGGCAAUAGCUUCAUUUU
..--.----..........-..(((...((((((.((((.(((.....)))))))..............((((((..((....))..))).))))))))))))........ ( -27.30)
>DroAna_CAF1 13136 110 + 1
AGACCUUCGACUAGCA-GAAAAACUUACAUUGCCAUCGCUCAUGCCAAGGGGCGAGUUAAGUAUAAAGUCUGUGGGUGCAAUUGCAUCCACGAGGGCGAUGGCCUCCUCCU
.....(((........-)))...........((((((((((.((((....))))................(((((((((....))))))))).))))))))))........ ( -38.60)
>consensus
AA__AUGCUUAUAGUA_AA_CUACUUACAUUGCCAUCGCUCAUGCCCAGAGGAGAGUUCAGAAUAAAAUCUGUGGGUGCAAUUGCAUCCACCAGAGCAAUGGCUUCGUUCU
.............................(((((...((....)).....)))))................(((((.((....)).)))))..((((....))))...... (-15.38 = -15.02 +  -0.36)

alignment

secondary structure

dotplot

Window 4

Location	6,445,262 – 6,445,369
Length	107
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.51
Mean single sequence MFE	-32.38
Consensus MFE	-18.53
Energy contribution	-18.78
Covariance contribution	0.25
Combinations/Pair	1.28
Mean z-score	-1.73
Structure conservation index	0.57
SVM decision value	0.80
SVM RNA-class probability	0.854459
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6445262 107 - 22407834
AGAACGAAGCCAUUGCUCUGGUGGAUGCCAUUGCUCCCACAGACUUUAUUCUAAACUCUCCUCUGGGCAUGAGCGAUGGAAACGUAAGUGG-UC-UACCAUAAGCAA--CU
............(((((.((((((((.(((((((((((.((((..................))))))...)))))))))..((....)).)-))-)))))..)))))--.. ( -34.27)
>DroVir_CAF1 28898 108 - 1
AGAACGAAGCGAUUGCUCUGGUGGAUGCUAUCGCACCCACGGAUUUCAUUCUCAAUUCUCCGCUGGGCAUGAGUGAUGGCAAUGUAUGUAG-CUGCGCUUUUUUUUU--UG
((((.((((((...(((...(((.((((((((((.((((((((...............)))).)))).....)))))))).)).)))..))-)..)))))).)))).--.. ( -32.76)
>DroGri_CAF1 26130 108 - 1
AGAAUGAAGCCAUUGCCUUGGUGGAUGCAAUUGCACCCACCGAUUUCGUUUUGAACUCGCCGCUGGGCAUGAGUGAUGGCAAUGUGAGUAA-CUGUUAUUUAAGCAU--UU
.(((((....((((((((((((((.(((....))).)))))))...........(((((((....)))..))))...)))))))((((((.-....))))))..)))--)) ( -34.60)
>DroYak_CAF1 14267 107 - 1
AGAACGAAGCUAUUGCUCUGGUGGAUGCCAUUGCUCCCACAGACUUUAUUCUAAACUCUCCUCUGGGCAUGAGCGAUGGAAACGUAAGUGA-UC-UACUAAAAGCAA--CC
............(((((.((((((((.(((((((((((.((((..................))))))...)))))))))..((....)).)-))-)))))..)))))--.. ( -31.87)
>DroMoj_CAF1 38598 104 - 1
AAAAUGAAGCUAUUGCCCUGGUGGAUGCAAUUGCGCCCACAGAUUUCAUUUUGAACUCGCCAUUGGGCAUGAGCGAUGGCAAUGUAAGCAG-UUAUAAAAUA----U--UU
........((((((((....((((.(((....))).)))).((.(((.....))).))(((....)))....))))))))...........-..........----.--.. ( -27.40)
>DroAna_CAF1 13136 110 - 1
AGGAGGAGGCCAUCGCCCUCGUGGAUGCAAUUGCACCCACAGACUUUAUACUUAACUCGCCCCUUGGCAUGAGCGAUGGCAAUGUAAGUUUUUC-UGCUAGUCGAAGGUCU
((.(((((((((((((....((((.(((....))).))))..................(((....)))....))))))))(((....)))))))-).))((.(....).)) ( -33.40)
>consensus
AGAACGAAGCCAUUGCCCUGGUGGAUGCAAUUGCACCCACAGACUUCAUUCUAAACUCGCCGCUGGGCAUGAGCGAUGGCAAUGUAAGUAG_UC_UACUAUAAGCAU__CU
........((((((((....((((.(((....))).))))...............(((......))).....))))))))............................... (-18.53 = -18.78 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:29 2006