Locus 521

Sequence ID	3L_DroMel_CAF1
Location	1,531,712 – 1,531,908
Length	196
Max. P	0.998905

overview

Window 9

Location	1,531,712 – 1,531,828
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.63
Mean single sequence MFE	-37.98
Consensus MFE	-30.08
Energy contribution	-28.92
Covariance contribution	-1.16
Combinations/Pair	1.26
Mean z-score	-1.85
Structure conservation index	0.79
SVM decision value	0.86
SVM RNA-class probability	0.867953
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1531712 116 + 23771897
AAGAUCAGGCGGUGUGAUUGUCAGACAUGCAGGGUGUUUGUCGAGUGCUAACCAUAAUUAAAGGCGAAUUU----GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAAC
.......(((((..((((((.(((((((.....))))))).)))..((((..........((((((....)----))))).((((((....))))))....)))))))...))))).... ( -38.00)
>DroSec_CAF1 10521 116 + 1
AAGAUCGGGCGGUGCGUUUAUCAGACAUGCAGGGUGUUUGCCGAGUGCUAACCACAAUUAAAGGCGAAUUG----GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAAC
.......(((((.(((......((((((.....))))))((((.((..............(((((......----))))).((((((....)))))).)).)))).)))..))))).... ( -36.80)
>DroSim_CAF1 10648 116 + 1
AAGAUCGGGCGGUGCGAUUAUCAGACAUGCAGGGUGUUUGCCGAGUGCUAACCAUAAUUAAAGGCGAAUUG----GUCUUAUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAAC
.......(((((.((((.....((((((.....))))))((((.((..............(((((......----))))).((((((....)))))).)).))))))))..))))).... ( -40.40)
>DroEre_CAF1 10536 116 + 1
AAGAUCAGGCGGUGCGAUUAUCGCGCUUGCUGGGUGUUUGCUGAGUGCUAACCAUAAUUAAAGGUAAAUGU----GUCUUAUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAAC
.......(((((.((((.....((((((((.........)).))))))..(((.........)))...(((----((....((((((....)))))).)))))..))))..))))).... ( -38.80)
>DroYak_CAF1 10730 120 + 1
AAGAUCGGGCGGUGUGAUUAUCGGGCUUGCAGCGUGUUUGCUAAGUGCUAACCAUAAUUAAAGGUGAAUUUACCAGUCUUAUCGCUGGUAACAGUGAAACAUGGCCCGUUUCCGCCAAGC
..((.(((((.((((((((...(.((((((((.....)))).)))).)..............((((....))))))))...((((((....)))))).)))).)))))..))........ ( -35.90)
>consensus
AAGAUCGGGCGGUGCGAUUAUCAGACAUGCAGGGUGUUUGCCGAGUGCUAACCAUAAUUAAAGGCGAAUUU____GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAAC
.......(((((.(((......((((((.....))))))((((.((..............(((((..........))))).((((((....)))))).)).)))).)))..))))).... (-30.08 = -28.92 +  -1.16)

alignment

secondary structure

dotplot

Window 0

Location	1,531,752 – 1,531,868
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.03
Mean single sequence MFE	-32.68
Consensus MFE	-27.28
Energy contribution	-27.08
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.83
SVM decision value	0.37
SVM RNA-class probability	0.708753
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1531752 116 + 23771897
UCGAGUGCUAACCAUAAUUAAAGGCGAAUUU----GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCG
..((((((............((((((....)----))))).((((((....))))))....((((........))))...))))))((((((..(((........).))..))))))... ( -32.90)
>DroSec_CAF1 10561 116 + 1
CCGAGUGCUAACCACAAUUAAAGGCGAAUUG----GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCG
..((((((............(((((......----))))).((((((....))))))....((((........))))...))))))((((((..(((........).))..))))))... ( -33.00)
>DroSim_CAF1 10688 116 + 1
CCGAGUGCUAACCAUAAUUAAAGGCGAAUUG----GUCUUAUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCG
.(((((.((............))((((((((----....((((((((....))))(((((((((..(((((.....)))))......)))))))))..))))....)))))))).))))) ( -32.50)
>DroEre_CAF1 10576 116 + 1
CUGAGUGCUAACCAUAAUUAAAGGUAAAUGU----GUCUUAUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACUCGCGAUUCGCGUUUCG
..((((((..............(((((((((----((....((((((....)))))).....(((........)))..)))))))))))(((((....)))))..)).))))........ ( -35.00)
>DroYak_CAF1 10770 120 + 1
CUAAGUGCUAACCAUAAUUAAAGGUGAAUUUACCAGUCUUAUCGCUGGUAACAGUGAAACAUGGCCCGUUUCCGCCAAGCGCAUUUAUCGUGUUUCCAGAUACUCGCGAUUCGCGAUUCG
....(((((.............((((....)))).......((((((....))))))....((((........))))))))).......(((((....)))))(((((...))))).... ( -30.00)
>consensus
CCGAGUGCUAACCAUAAUUAAAGGCGAAUUU____GUCUUAUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCG
..((((((............(((((..........))))).((((((....)))))).....(((........)))....))))))((((((..(((........).))..))))))... (-27.28 = -27.08 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	1,531,788 – 1,531,908
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.33
Mean single sequence MFE	-41.76
Consensus MFE	-38.08
Energy contribution	-38.96
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-2.15
Structure conservation index	0.91
SVM decision value	3.28
SVM RNA-class probability	0.998905
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1531788 120 + 23771897
AUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCGAGUGCAGCGGAAGCGGCCGUCAGGCGCAGAAAUAUUGUUC
.((((((....))))))...(((((.(((((((((.....((((((((((((..(((........).))..))))))..)))))).)))))))))))))).................... ( -46.30)
>DroSec_CAF1 10597 120 + 1
AUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCGAGUGCAGCGGAAGCGACCGUCAGGCGCAGAAAUAUUGUUC
.((((((....))))))...((((.((((((((((.....((((((((((((..(((........).))..))))))..)))))).)))))))))))))).................... ( -44.20)
>DroSim_CAF1 10724 120 + 1
AUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCGAGUGCAGCGGAAGCGACCGUCAGGCGCAGAAAUAUUGUUC
.((((((....))))))...((((.((((((((((.....((((((((((((..(((........).))..))))))..)))))).)))))))))))))).................... ( -46.00)
>DroEre_CAF1 10612 120 + 1
AUCGCUGGAAACAGUGAAACACGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACUCGCGAUUCGCGUUUCGAGUGCAACGGAAGAGCCCGUCACCCACAUAAAUAUGGUUC
.((((((....)))))).....(((((...((((..((((((.......))))))...(.((((((.(((....))).)))))))..)))).)))))......(((........)))... ( -36.30)
>DroYak_CAF1 10810 120 + 1
AUCGCUGGUAACAGUGAAACAUGGCCCGUUUCCGCCAAGCGCAUUUAUCGUGUUUCCAGAUACUCGCGAUUCGCGAUUCGAGUGCAACGGAAGCGCCCGUCAGCCGCAGAAAUAUUGUUC
.((((((....))))))....((((.((((((((....((((....((((((..(((........).))..))))))....))))..))))))))...)))).................. ( -36.00)
>consensus
AUCGCUGGAAACAGUGAAACAUGGCUCGUUUCCGCCAAACGCAUUUAUCGUGUUUCCAGAUACCCGCGAUUCGCGAUUCGAGUGCAGCGGAAGCGACCGUCAGGCGCAGAAAUAUUGUUC
.((((((....))))))...((((.((((((((((.....((((((((((((..(((........).))..))))))..)))))).)))))))))))))).................... (-38.08 = -38.96 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:09 2006