Locus 1355

Sequence ID	2L_DroMel_CAF1
Location	3,594,367 – 3,594,514
Length	147
Max. P	0.999048

overview

Window 6

Location	3,594,367 – 3,594,486
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.60
Mean single sequence MFE	-31.07
Consensus MFE	-28.11
Energy contribution	-28.11
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.90
SVM decision value	2.78
SVM RNA-class probability	0.996961
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3594367 119 + 22407834
-CAGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
-.((((((...((((...(((((((..((((((((((.(.....).)))))))..................((((......))))...)))...)))))))..))))....))))))... ( -30.90)
>DroVir_CAF1 74863 112 + 1
--------UACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
--------.....(((((((.((((((((((((((((.(.....).)))))))..................((((......))))...))).......)))))).)))))))........ ( -28.11)
>DroGri_CAF1 76511 120 + 1
CGAGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
..((((((...((((...(((((((..((((((((((.(.....).)))))))..................((((......))))...)))...)))))))..))))....))))))... ( -31.00)
>DroEre_CAF1 63888 119 + 1
-CAGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
-.((((((...((((...(((((((..((((((((((.(.....).)))))))..................((((......))))...)))...)))))))..))))....))))))... ( -30.90)
>DroWil_CAF1 93269 119 + 1
-GUGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGUGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
-..(((((...((((...(((((((..((((((((((((.....)))))))))..................((((......))))...)))...)))))))..))))....))))).... ( -34.30)
>DroMoj_CAF1 83129 120 + 1
CGGGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
.((((.....))))((((((.((((((((((((((((.(.....).)))))))..................((((......))))...))).......)))))).))))))......... ( -31.21)
>consensus
_GAGGCACUACUCCGAUAUCAGUUUUAUGGGUGGCCCACAUGUCGAGGGCCAUAAAGUAGAAAAUUAUCACCUUUUAAAUUGAAGAAUCCAAACAAAUUGAAACGGAUAUCGUGUUUAAG
.............(((((((.((((((((((((((((.(.....).)))))))..................((((......))))...))).......)))))).)))))))........ (-28.11 = -28.11 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	3,594,367 – 3,594,486
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.60
Mean single sequence MFE	-29.72
Consensus MFE	-27.88
Energy contribution	-28.38
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.94
SVM decision value	3.34
SVM RNA-class probability	0.999048
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3594367 119 - 22407834
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCUG-
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((.(.....).)))))).)))..))).)))...))))...)))....- ( -29.60)
>DroVir_CAF1 74863 112 - 1
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUA--------
.....((.(((((((.((((.........(((..............(((((((......)).))))).((((((.(.....).)))))).)))..)))).)))))))..)).-------- ( -26.30)
>DroGri_CAF1 76511 120 - 1
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCUCG
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((.(.....).)))))).)))..))).)))...))))...)))..... ( -29.60)
>DroEre_CAF1 63888 119 - 1
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCUG-
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((.(.....).)))))).)))..))).)))...))))...)))....- ( -29.60)
>DroWil_CAF1 93269 119 - 1
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCACGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCAC-
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((((.....)))))))).)))..))).)))...))))...)))....- ( -33.60)
>DroMoj_CAF1 83129 120 - 1
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCCCG
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((.(.....).)))))).)))..))).)))...))))...)))..... ( -29.60)
>consensus
CUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACAUGUGGGCCACCCAUAAAACUGAUAUCGGAGUAGUGCCUC_
......(((....((((..(((.(((...(((..............(((((((......)).))))).((((((.(.....).)))))).)))..))).)))...))))...)))..... (-27.88 = -28.38 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	3,594,406 – 3,594,514
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.36
Mean single sequence MFE	-23.65
Consensus MFE	-22.81
Energy contribution	-22.97
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.12
Structure conservation index	0.96
SVM decision value	1.20
SVM RNA-class probability	0.929598
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3594406 108 - 22407834
------------AGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
------------(((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).)))))))..... ( -24.24)
>DroVir_CAF1 74895 108 - 1
------------UGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
------------.((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).))))))...... ( -23.74)
>DroGri_CAF1 76551 108 - 1
------------UGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
------------.((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).))))))...... ( -23.74)
>DroWil_CAF1 93308 120 - 1
UUCUGUUUCCUUUUGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCACGACA
(((((((.((....))..)))))))....(((((...............((.(((((...(.....)..)))))...)).........(((.((((.........)))).)))..))))) ( -22.20)
>DroMoj_CAF1 83169 108 - 1
------------UGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
------------.((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).))))))...... ( -23.74)
>DroPer_CAF1 69066 108 - 1
------------AGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
------------(((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).)))))))..... ( -24.24)
>consensus
____________UGGGCUAAUAGAAGUGAUGUCGAUAGCACUUAAACACGAUAUCCGUUUCAAUUUGUUUGGAUUCUUCAAUUUAAAAGGUGAUAAUUUUCUACUUUAUGGCCCUCGACA
.............((((((...((((.(((((((..............)))))))...(((((.....)))))..)))).......(((((((......)).))))).))))))...... (-22.81 = -22.97 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:31 2006