Locus 3020

Sequence ID	2L_DroMel_CAF1
Location	8,616,799 – 8,617,091
Length	292
Max. P	0.933123

overview

Window 4

Location	8,616,799 – 8,616,904
Length	105
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	88.30
Mean single sequence MFE	-25.00
Consensus MFE	-17.39
Energy contribution	-19.83
Covariance contribution	2.45
Combinations/Pair	1.03
Mean z-score	-2.26
Structure conservation index	0.70
SVM decision value	-0.02
SVM RNA-class probability	0.522385
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8616799 105 + 22407834
UUUAUUAACAGAUACAACUUUCUUUAUAUGGGGUUUAAUCCUAAUGCUACCAUAGAUACAAACCAAAAGAUUUAUGGAGCAAUCUCGCUGUCAGUUUCUCCUGU---------A
.......((((....((((..(......((((((...)))))).((((.((((((((............))))))))))))........)..))))....))))---------. ( -19.80)
>DroSec_CAF1 45088 114 + 1
UUUAUUAUCAGAUAGAUACUUCUUUAUAUGAGGUUUAAUCCUAAUGCUGCCAUAGAUUUAAACCAAAAGAUUUAUGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUA
..........(((.((.(((((.......))))))).)))....((((.((((((((((........))))))))))))))..((((((..(((......)))...)))))).. ( -28.60)
>DroSim_CAF1 50774 114 + 1
UUUAUUAUCAGAUAGAUACUUCUUUAUAUGAGCUUUAAUCCUAAUGCUGCCAUAGAUUUAAACCAAAAGAUUUAUGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUA
.......(((.(((((......))))).))).............((((.((((((((((........))))))))))))))..((((((..(((......)))...)))))).. ( -26.60)
>consensus
UUUAUUAUCAGAUAGAUACUUCUUUAUAUGAGGUUUAAUCCUAAUGCUGCCAUAGAUUUAAACCAAAAGAUUUAUGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUA
(((((....(((........)))....)))))............((((.((((((((((........))))))))))))))..((((((..(((......)))...)))))).. (-17.39 = -19.83 +   2.45)

alignment

secondary structure

dotplot

Window 5

Location	8,616,873 – 8,616,983
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.58
Mean single sequence MFE	-28.60
Consensus MFE	-14.66
Energy contribution	-16.10
Covariance contribution	1.44
Combinations/Pair	1.19
Mean z-score	-2.02
Structure conservation index	0.51
SVM decision value	0.81
SVM RNA-class probability	0.855317
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8616873 110 + 22407834
UGGAGCAAUCUCGCUGUCAGUUUCUCCUGU---------ACUAGUUAGAUAGUUGGAUUUACCCCAUCUCCCUUUUGAUAAUGUUCCUCUAAAAU-UUCCCGAGAUGGUCUUCUAUCUCG
.((((((((((.((((((((......))).---------)).))).))))((.(((.......))).))............))))))........-....((((((((....)))))))) ( -27.60)
>DroSec_CAF1 45162 118 + 1
UGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUACUA-UUGGUUAGUUGGAUUCC-CCCACCUGCCUUUUGGUGAUUUUCCUUUUAAAUUUUCCCGAGAUGGUCUUCUAUCUCG
.((((.(((((((((..(((......)))...)))))..((((-..(((.((.(((.....-.))).)))))...)))))))))))).............((((((((....)))))))) ( -33.10)
>DroSim_CAF1 50848 118 + 1
UGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUACUA-UUGGAUAGUUGGAUUCCCCCCACCUGCCUUUUGGUGAUGUUCCUCUGAAAU-UUCCCGAGAUGGUCUUCUAUCUCG
.((((((..((((((..(((......)))...))))))(((((-..((.(((.(((.......))).)))))...))))).))))))........-....((((((((....)))))))) ( -37.60)
>DroEre_CAF1 46808 102 + 1
UGGC---------------GUUUCUCCCGCAAAGUUUAUACCA-UCGGAUAGUUGGACUUACCCCACAUCCC-UCUGGUAAUAUUCCCCCCAAAU-UUCCCGAGAUGGUAUUCUAUCUCG
..((---------------(.......)))........(((((-..((((.((.((......)).)))))).-..)))))...............-....((((((((....)))))))) ( -24.40)
>DroYak_CAF1 48077 117 + 1
UGGAGUAAGCCCGCAGACAGUUUCGCCUGUAAAGUGUUUACUA-UCGAAUAGCUAGAUUUACCCUACAUCCC-UUUGGUAAUAUUUCUCUUAAAU-UUCCCGAGAUGGUAUUCUAUCGCG
.(((((((((.(....((((......))))...).))))))).-)).....((((((..((((...((....-..))........((((......-.....)))).)))).))))..)). ( -20.30)
>consensus
UGGAGCAAUCACGCUGUCAGUUUCUCCUGUAAAGUGUGUACUA_UUGGAUAGUUGGAUUUACCCCACCUCCCUUUUGGUAAUAUUCCUCUUAAAU_UUCCCGAGAUGGUCUUCUAUCUCG
.((((((..........(((......))).........(((((...((.....(((.......)))....))...))))).)))))).............((((((((....)))))))) (-14.66 = -16.10 +   1.44)

alignment

secondary structure

dotplot

Window 6

Location	8,616,983 – 8,617,091
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.67
Mean single sequence MFE	-39.88
Consensus MFE	-37.06
Energy contribution	-37.70
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.47
Structure conservation index	0.93
SVM decision value	1.23
SVM RNA-class probability	0.933123
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8616983 108 - 22407834
CGUGCUCGAGUGGCAUCGCCCUUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAUCUCACGCUCCAUUCAGGCAAUCAGUAUGGCAGCUACUUGUGGUCCUGCA
..(((..(((((((((.(((((((..(((....))).)))).)))..))))(((((.....)))))..)))))..)))....(((.(((.((.....)).))).))). ( -39.70)
>DroSec_CAF1 45280 108 - 1
CGUGCUCGAGUGGCAUCGCCCUUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAGCUCACGCUCCAUUCAGGCAAUCAGUAUGGCAGCUACUUGCGGUCCUGCA
..(((..(((((((((.(((((((..(((....))).)))).)))..))))(((((.....)))))..)))))..)))....(((.(((.((.....)).))).))). ( -41.30)
>DroSim_CAF1 50966 108 - 1
CGUGCUCGAGUGGCAUCGCCCUUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAGCUCACGCUCCAUUCAGGCAAUCAGUAUGGCAGCUACUUGCGGUCCUGCA
..(((..(((((((((.(((((((..(((....))).)))).)))..))))(((((.....)))))..)))))..)))....(((.(((.((.....)).))).))). ( -41.30)
>DroEre_CAF1 46910 107 - 1
CGUGCUCGAGUGGCAUCGC-CGUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAGCUCACGCUACAUUCGGGCAAUCGGUAUGGCAGCUACUUGCGGUCCUGCA
..((((((((((((((.((-(.(((.(((....)))...))))))..))))(((((.....)))))..))))))))))....(((.(((.((.....)).))).))). ( -43.20)
>DroYak_CAF1 48194 108 - 1
CGUGCUCGAGUGGCAUCGCCCGUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAGCUCACGCUACAUUCAGGCAAUCAGUAUGGCAGCUACUUGCGGUCCUUCA
..(((..(((((((((.((((.((..(((....))).)).).)))..))))(((((.....)))))..)))))..)))........(((.((.....)).)))..... ( -33.90)
>consensus
CGUGCUCGAGUGGCAUCGCCCUUCUACAGGUGACUGCGAAGAGGUUUAUGCGUGUGAAGCUCACGCUCCAUUCAGGCAAUCAGUAUGGCAGCUACUUGCGGUCCUGCA
..((((.(((((((((.(((((((..(((....))).)))).)))..))))(((((.....)))))..))))).))))....(((.(((.((.....)).))).))). (-37.06 = -37.70 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:21 2006