Locus 4107

Sequence ID	3R_DroMel_CAF1
Location	11,209,382 – 11,209,518
Length	136
Max. P	0.958607

overview

Window 5

Location	11,209,382 – 11,209,501
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.72
Mean single sequence MFE	-27.87
Consensus MFE	-24.19
Energy contribution	-24.80
Covariance contribution	0.61
Combinations/Pair	1.03
Mean z-score	-2.27
Structure conservation index	0.87
SVM decision value	1.49
SVM RNA-class probability	0.958607
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11209382 119 + 27905053
AGUGGAAUCACUGGCAUUCCACCCCUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCACCUAUUUUCAAUCGCAAUGAACUACGAACAACAACA-
.((((....(((((((.........))))))).....((((..((((((((((((((((...)))))..))))((((.....))))...))).))))...))))))))...........- ( -30.40)
>DroPse_CAF1 16202 117 + 1
AGUGGCAUCACUGGCAUCCCACCAUUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUCGCAAUGCAU--CUAACUACAACA-
(((.((((.(((((((.........)))))))...........((((((((((((((((...)))))..)))).((....)).......))).))))..))))..--...)))......- ( -27.80)
>DroGri_CAF1 12220 120 + 1
AGUGGAAUAUCUGGCAUUCCACCAUUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAAUUAUUUUCAAUUGCAAUGAACUACAAGCAACAAAAA
.(((((((((((((((.........))))))...)))))).)))..(((((((((((((...)))))..)))).((....)).......)))).((((............))))...... ( -29.10)
>DroWil_CAF1 14831 116 + 1
AGUGGAAUCACUGGCAUUCCACCAUUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUUGCAAUGAACUA---ACAACAAGA-
.((((((((....).)))))))((((((((((........)).)).(((((((((((((...)))))..)))).((....)).......))))...)))))).....---.........- ( -26.60)
>DroAna_CAF1 11715 119 + 1
AGUGGAAUCUCUGGCAUUCCACCUCUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCGACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUCACAAUGAACUAACAACAGCAACA-
.(((((((..((((((.........)))))).....)))).)))(((((((((((((((...)))))..)))).((....)).......))).))).......................- ( -25.50)
>DroPer_CAF1 16776 117 + 1
AGUGGCAUCACUGGCAUCCCACCAUUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUCGCAAUGCAU--CUAACUACAACA-
(((.((((.(((((((.........)))))))...........((((((((((((((((...)))))..)))).((....)).......))).))))..))))..--...)))......- ( -27.80)
>consensus
AGUGGAAUCACUGGCAUUCCACCAUUGCCGGUAAAUAUUCACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUCGCAAUGAACUACUAACAACAACA_
.(((((...(((((((.........))))))).....))))).((((((((((((((((...)))))..)))).((....)).......))).))))....................... (-24.19 = -24.80 +   0.61)

alignment

secondary structure

dotplot

Window 6

Location	11,209,422 – 11,209,518
Length	96
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	83.52
Mean single sequence MFE	-15.27
Consensus MFE	-12.22
Energy contribution	-12.17
Covariance contribution	-0.05
Combinations/Pair	1.06
Mean z-score	-1.48
Structure conservation index	0.80
SVM decision value	0.04
SVM RNA-class probability	0.554855
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11209422 96 + 27905053
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCACCUAUUUUCAAUCGCAAUGAACUACGAACAACAACA--GCAACC--ACA----GCAA-UUAU
...((((((((((((((((...)))))..))))((((.....))))...))).))))......................--((....--...----))..-.... ( -16.40)
>DroVir_CAF1 10998 101 + 1
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUUGCAAUGAACUACAAGCAACAAAAACGAAACCCAACAA---ACAA-UUAU
...((.(((((((((((((...)))))..)))).((....)).......)))).((((............))))......))...........---....-.... ( -14.30)
>DroGri_CAF1 12260 101 + 1
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAAUUAUUUUCAAUUGCAAUGAACUACAAGCAACAAAAAAGCAUCAAAAAAA---AAAA-AUAA
....((((..(((((((((...)))))..)))).((....))............((((............))))........)))).......---....-.... ( -15.30)
>DroWil_CAF1 14871 96 + 1
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUUGCAAUGAACUA---ACAACAAGA--GCAACU--GCA-ACUGCAA-CUCA
......(((((((((((((...)))))..)))).((....)).......)))).(((((.((.....---.))......--((....--)).-..)))))-.... ( -16.30)
>DroMoj_CAF1 11139 95 + 1
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUUGCAAUGAACUACAAGCAACAAAU--GAAA---AAUAU---ACUA-U-AU
..........(((((((((...)))))..)))).((....)).....((((((.((((............))))....)--))))---)....---....-.-.. ( -14.20)
>DroAna_CAF1 11755 96 + 1
ACACGAUGAAGGCUAUGCCGACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUCACAAUGAACUAACAACAGCAACA--GCAACC--ACA----GCCAAAUA-
..........(((((((((...))))).......(((............((((.......)))).........((....--)).)))--..)----))).....- ( -15.10)
>consensus
ACACGAUGAAGGCUAUGCCAACGGCAUUAAGUCAGGUAAACCAACUAUUUUCAAUUGCAAUGAACUACAAACAACAAAA__GCAACC__ACA____ACAA_UUAU
...((((((((((((((((...)))))..)))).((....)).......))).))))................................................ (-12.22 = -12.17 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:17 2006