Locus 1438

Sequence ID	2L_DroMel_CAF1
Location	3,825,330 – 3,825,434
Length	104
Max. P	0.947797

overview

Window 1

Location	3,825,330 – 3,825,434
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	74.98
Mean single sequence MFE	-24.20
Consensus MFE	-15.81
Energy contribution	-15.15
Covariance contribution	-0.66
Combinations/Pair	1.19
Mean z-score	-1.77
Structure conservation index	0.65
SVM decision value	1.38
SVM RNA-class probability	0.947797
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3825330 104 + 22407834
ACCCCAAAAUACCGACCCUGUUUGGAUUGGAUGUAAUGGAUAUUUUGACGCCGAAGCA-GCAAAAGACUGCAAAUAAACAUCCACAAGUUCCCAAACA--------------A-CGUCUA
.............(((..(((((((..(((((((..(((...........)))..(((-((....).))))......))))))).......)))))))--------------.-.))).. ( -24.00)
>DroVir_CAF1 30820 100 + 1
AC-------------CCCUGUUUGGAUUGGAUGUAAUGGAUAUUUUGACGCCGAGCCAAGCAAAGGGCUGCAAAUAAACAUCCACAAGUUCCAAAACAAACGGC-------AGCCAGCAC
..-------------..(((((((..(((((.....(((((.(((....((..((((........))))))....))).))))).....)))))..))))))).-------......... ( -27.10)
>DroGri_CAF1 18147 98 + 1
AC-------------CCCUGUUUGGAUUGGAUGUAAUGGAUAUUUUGACGCCGAUGCAUGCAAAGGGCUGCAAAUAAACAUCCACAAGUUCCAAAACACGCG-C-------AA-CGCCAA
..-------------...((((((((.(((((((..(((...........))).((((.((.....)))))).....))))))).....))).))))).(((-.-------..-)))... ( -21.50)
>DroWil_CAF1 34974 97 + 1
AGCCAAA------AACUGUGUUUGGAUUGGAUGUAAUAGAUAUUUUGACGCUGAAGCA-ACUAAAAACGGCAAAUAAACAUCCACAAAAUCCAAAAUA--------------A-AA-AUA
.......------.......((((((((((((((....((....))...((((.....-........))))......)))))))....)))))))...--------------.-..-... ( -16.22)
>DroMoj_CAF1 20249 99 + 1
AC-------------CCCUGUUUGGAUUGGAUGUAAUGGAUAUUUUGACGCCGAGCCAAGCAAAGGGCUGCAAAUAAACAUCCACAAGUUCCAAAACAAACGGC-------AA-CAGCAA
..-------------..(((((((..(((((.....(((((.(((....((..((((........))))))....))).))))).....)))))..))))))).-------..-...... ( -27.10)
>DroAna_CAF1 15870 117 + 1
ACCCCAA-AGACCGACCCUGUUUGGAUUGGGUGUAAUGGAUAUUUUGACGCCGGAGCA-GCAAAAGACUGCAAAUAAACAUCCACACGUUCCCAAACACACGGUCCGCUUCCA-UGCCUC
.......-.(((((....(((((((...(..(((..(((((..((((....))))(((-((....).))))........))))).)))..))))))))..))))).((.....-.))... ( -29.30)
>consensus
AC_____________CCCUGUUUGGAUUGGAUGUAAUGGAUAUUUUGACGCCGAAGCA_GCAAAAGACUGCAAAUAAACAUCCACAAGUUCCAAAACA_ACG_C_______AA_CACCAA
..................((((((((.(((((((..(((...........)))......(((......)))......))))))).....))).)))))...................... (-15.81 = -15.15 +  -0.66)

alignment

secondary structure

dotplot

Window 2

Location	3,825,330 – 3,825,434
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.98
Mean single sequence MFE	-30.54
Consensus MFE	-16.34
Energy contribution	-17.23
Covariance contribution	0.89
Combinations/Pair	1.09
Mean z-score	-2.01
Structure conservation index	0.54
SVM decision value	1.12
SVM RNA-class probability	0.918489
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3825330 104 - 22407834
UAGACG-U--------------UGUUUGGGAACUUGUGGAUGUUUAUUUGCAGUCUUUUGC-UGCUUCGGCGUCAAAAUAUCCAUUACAUCCAAUCCAAACAGGGUCGGUAUUUUGGGGU
..(((.-(--------------((((((((.....((((((((((....((((....))))-.((....))....)))))))))).........))))))))).)))............. ( -33.04)
>DroVir_CAF1 30820 100 - 1
GUGCUGGCU-------GCCGUUUGUUUUGGAACUUGUGGAUGUUUAUUUGCAGCCCUUUGCUUGGCUCGGCGUCAAAAUAUCCAUUACAUCCAAUCCAAACAGGG-------------GU
......(((-------.(.(((((..(((((....((((((((((...(((((((........))))..)))...))))))))))....)))))..))))).).)-------------)) ( -34.40)
>DroGri_CAF1 18147 98 - 1
UUGGCG-UU-------G-CGCGUGUUUUGGAACUUGUGGAUGUUUAUUUGCAGCCCUUUGCAUGCAUCGGCGUCAAAAUAUCCAUUACAUCCAAUCCAAACAGGG-------------GU
((((((-((-------(-.((((((...((...(((..(((....)))..))).))...))))))..))))))))).................((((......))-------------)) ( -26.90)
>DroWil_CAF1 34974 97 - 1
UAU-UU-U--------------UAUUUUGGAUUUUGUGGAUGUUUAUUUGCCGUUUUUAGU-UGCUUCAGCGUCAAAAUAUCUAUUACAUCCAAUCCAAACACAGUU------UUUGGCU
...-..-.--------------....((((((...((((((((((...(((.((.......-.))....)))...))))))))))...)))))).(((((.......------))))).. ( -18.10)
>DroMoj_CAF1 20249 99 - 1
UUGCUG-UU-------GCCGUUUGUUUUGGAACUUGUGGAUGUUUAUUUGCAGCCCUUUGCUUGGCUCGGCGUCAAAAUAUCCAUUACAUCCAAUCCAAACAGGG-------------GU
......-..-------.(((((((..(((((....((((((((((...(((((((........))))..)))...))))))))))....)))))..))))).)).-------------.. ( -32.70)
>DroAna_CAF1 15870 117 - 1
GAGGCA-UGGAAGCGGACCGUGUGUUUGGGAACGUGUGGAUGUUUAUUUGCAGUCUUUUGC-UGCUCCGGCGUCAAAAUAUCCAUUACACCCAAUCCAAACAGGGUCGGUCU-UUGGGGU
...((.-(.(((((.((((.(((..(((((.....((((((((((....((((....))))-.((....))....))))))))))....))))).....))).)))).).))-)).).)) ( -38.10)
>consensus
UAGCCG_UU_______G_CGU_UGUUUUGGAACUUGUGGAUGUUUAUUUGCAGCCCUUUGC_UGCUUCGGCGUCAAAAUAUCCAUUACAUCCAAUCCAAACAGGG_____________GU
......................((..(((((....((((((((((....((((....))))..((....))....))))))))))....)))))..))...................... (-16.34 = -17.23 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:39 2006