Locus 856

Sequence ID	X_DroMel_CAF1
Location	2,432,712 – 2,432,886
Length	174
Max. P	0.961456

overview

Window 7

Location	2,432,712 – 2,432,809
Length	97
Sequences	3
Columns	117
Reading direction	forward
Mean pairwise identity	80.00
Mean single sequence MFE	-17.03
Consensus MFE	-14.49
Energy contribution	-14.82
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.06
Structure conservation index	0.85
SVM decision value	0.14
SVM RNA-class probability	0.601725
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432712 97 + 22224390
--ACAAUCGGACCGGAAAUGAUCCC----AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGCAAGCCAGCUGGAAACAGCACA--------------U
--....((((...(((.((((((..----...)))....(((.............)))))).)))..))))................((((....))))...--------------. ( -15.92)
>DroSim_CAF1 43908 96 + 1
--ACA-UCGGACCGGAAAUGCCCCC----AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA--------------U
--...-((((...(((.((((....----............................)))).)))..))))................((((....))))...--------------. ( -16.55)
>DroEre_CAF1 80486 116 + 1
UUACA-UCGGACUGGAAAUGCCCCCCAAAAAAGAUAACCCAAAACCCGAUUAAUCCUGCAUCUCCCAUCGACUCACAAAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAU
.((((-((((...(((.((((....................................)))).)))..))))............((..((((....)))))).......))))..... ( -18.62)
>consensus
__ACA_UCGGACCGGAAAUGCCCCC____AAAGAUAACCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA______________U
......((((...(((.((((....................................)))).)))..))))................((((....)))).................. (-14.49 = -14.82 +   0.33)

alignment

secondary structure

dotplot

Window 8

Location	2,432,743 – 2,432,846
Length	103
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-17.45
Consensus MFE	-13.97
Energy contribution	-13.97
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.24
Structure conservation index	0.80
SVM decision value	1.53
SVM RNA-class probability	0.961456
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432743 103 + 22224390
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGCAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAAUA-CCCCAACAAAAUAUCGCAGU--UCUUAUA
...(((((.(((.((((..(((....................))).....((((....))))...--------------...........-.........)))))))..))--))).... ( -15.45)
>DroSim_CAF1 43938 103 + 1
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAUUA-CCCCAACAAAAUAUCGCAGU--UCUAAUC
...(((((.(((.((((.................................((((....))))((.--------------...))......-.........)))))))..))--))).... ( -14.80)
>DroEre_CAF1 80522 120 + 1
CCCAAAACCCGAUUAAUCCUGCAUCUCCCAUCGACUCACAAAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAUAUGUAAAUUUCCCCCAACAAAAUAUUGCAGAUAUCUAAUU
..................(((((.......................((..((((....)))))).((((((((....))))))))....................))))).......... ( -22.10)
>consensus
CCCAGAACCCGACUAUUCCUGCAUCUCCCAUCGACCCACCAAGAAAGCCAGCUGGAAACAGCACA______________UAUGUAAAUUA_CCCCAACAAAAUAUCGCAGU__UCUAAUA
..................((((............................((((....))))...................(((............))).......)))).......... (-13.97 = -13.97 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	2,432,783 – 2,432,886
Length	103
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-20.13
Consensus MFE	-14.48
Energy contribution	-14.03
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.72
SVM decision value	0.00
SVM RNA-class probability	0.534241
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2432783 103 + 22224390
AAGCAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAAUA-CCCCAACAAAAUAUCGCAGU--UCUUAUACCCAAGAUCAUUUUGAACAGAAAGUAAGCUCAUUGUUUUG
((((((((..((((....))))...--------------...........-......(((((((((...((--......))....))).))))))............)))...))))).. ( -17.20)
>DroSim_CAF1 43978 103 + 1
AAGAAAGCCAGCUGGAAACAGCACA--------------UAUGUAAAUUA-CCCCAACAAAAUAUCGCAGU--UCUAAUCCCCAAGAUCAUUUCGAACAGAAAGUAAGCUCAUUGUUUUG
..........((((....))))...--------------...........-......(((((((..((.(.--(((........))).).((((.....))))....))....))))))) ( -16.40)
>DroEre_CAF1 80562 119 + 1
AAGAAAGCAAGCUGGAGACAGCGCAUACAUAUGUACAUAUAUGUAAAUUUCCCCCAACAAAAUAUUGCAGAUAUCUAAUUCCUAAGAUCAUUUCGAACCGAAAGUAAGCUCAUGGUUUU-
..((((((((((((....))))...((((((((....))))))))...................))))....((((........))))..))))((((((..((....))..)))))).- ( -26.80)
>consensus
AAGAAAGCCAGCUGGAAACAGCACA______________UAUGUAAAUUA_CCCCAACAAAAUAUCGCAGU__UCUAAUACCCAAGAUCAUUUCGAACAGAAAGUAAGCUCAUUGUUUUG
......((..((((....))))...................(((............))).......))..........................((((((..((....))..)))))).. (-14.48 = -14.03 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:23 2006