Locus 678

Sequence ID	2R_DroMel_CAF1
Location	3,349,673 – 3,349,808
Length	135
Max. P	0.999979

overview

Window 6

Location	3,349,673 – 3,349,769
Length	96
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	92.04
Mean single sequence MFE	-26.04
Consensus MFE	-22.06
Energy contribution	-22.50
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.85
SVM decision value	1.75
SVM RNA-class probability	0.975674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3349673 96 + 20766785
UUUGCCAUUCAGACUUUCCCAGAAAUCUCAAUUAGAUUGACACUCCUGCCAUGGCUGCCAUGGCAAACCACUUGGAUUGGA-----UCCGAUUGGCCCAAC
...((((.((.((((.(((.((.(((((.....)))))........((((((((...)))))))).....)).)))..)).-----)).)).))))..... ( -27.80)
>DroSec_CAF1 10224 96 + 1
UUUGCCAUUCAGACUUUCCCAGAAAUCUCAAUUAGAUUGACACUCCUGCCAUGGCUGCCAUGGCAAACCACUUGGAUUGGA-----UCCGAUUGGCCCAAC
...((((.((.((((.(((.((.(((((.....)))))........((((((((...)))))))).....)).)))..)).-----)).)).))))..... ( -27.80)
>DroSim_CAF1 3369 96 + 1
UUUGCCAUUCAGACUUUCCCAGAAAUCUCAAUUAGAUUGACACUCCUGCCAUGGCUGCCAUGGCAAACCACUUGGAUUGGA-----UCCGAUUGGUCCAAC
...((((.((.((((.(((.((.(((((.....)))))........((((((((...)))))))).....)).)))..)).-----)).)).))))..... ( -25.90)
>DroEre_CAF1 1474 101 + 1
UUUGCCAUUCAGACUUUCCCAGAAAUCUCAAUUAGAUUGACACUCCUACCAUGGCUGCCAUGGCAAUGCAAUUGGAUUGGAUUUGUUCGGAUUGGCCCGAC
...((((.((.((.......(.(((((.(((((.(((((.((......((((((...))))))...))))))).)))))))))).))).)).))))..... ( -24.81)
>DroYak_CAF1 4854 96 + 1
UUUGCCAUUCAGACUUGCCCAGAAAUCUCAAUUAGAUUGACAGUCCUGCCACGGCUGCCAUGGCAAUGCACUUGGAUUGAA-----UCGGAUUGGCUGAAC
...((((.((.((..........(((((.....)))))..(((((((((((.((...)).)))))........))))))..-----)).)).))))..... ( -23.90)
>consensus
UUUGCCAUUCAGACUUUCCCAGAAAUCUCAAUUAGAUUGACACUCCUGCCAUGGCUGCCAUGGCAAACCACUUGGAUUGGA_____UCCGAUUGGCCCAAC
...((((.((.((.....((((.(((((.....))))).....(((((((((((...))))))))........)))))))......)).)).))))..... (-22.06 = -22.50 +   0.44)

alignment

secondary structure

dotplot

Window 7

Location	3,349,673 – 3,349,769
Length	96
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	92.04
Mean single sequence MFE	-33.62
Consensus MFE	-31.70
Energy contribution	-32.02
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-2.96
Structure conservation index	0.94
SVM decision value	5.20
SVM RNA-class probability	0.999979
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3349673 96 - 20766785
GUUGGGCCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUUCUGGGAAAGUCUGAAUGGCAAA
.....((((.(((((-----(....(((..((((((.((....))))))))..(((((((.(((((...))))).))))))))))..)))))).))))... ( -37.50)
>DroSec_CAF1 10224 96 - 1
GUUGGGCCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUUCUGGGAAAGUCUGAAUGGCAAA
.....((((.(((((-----(....(((..((((((.((....))))))))..(((((((.(((((...))))).))))))))))..)))))).))))... ( -37.50)
>DroSim_CAF1 3369 96 - 1
GUUGGACCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUUCUGGGAAAGUCUGAAUGGCAAA
....(.(((.(((((-----(....(((..((((((.((....))))))))..(((((((.(((((...))))).))))))))))..)))))).))))... ( -33.70)
>DroEre_CAF1 1474 101 - 1
GUCGGGCCAAUCCGAACAAAUCCAAUCCAAUUGCAUUGCCAUGGCAGCCAUGGUAGGAGUGUCAAUCUAAUUGAGAUUUCUGGGAAAGUCUGAAUGGCAAA
.....((((.((.((.....((((............((((((((...))))))))(((((.(((((...))))).)))))))))....)).)).))))... ( -29.80)
>DroYak_CAF1 4854 96 - 1
GUUCAGCCAAUCCGA-----UUCAAUCCAAGUGCAUUGCCAUGGCAGCCGUGGCAGGACUGUCAAUCUAAUUGAGAUUUCUGGGCAAGUCUGAAUGGCAAA
.....((((.((.((-----((...(((((((.(..((((((((...))))))))).)))...(((((.....)))))..))))..)))).)).))))... ( -29.60)
>consensus
GUUGGGCCAAUCGGA_____UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUUCUGGGAAAGUCUGAAUGGCAAA
.....((((.(((((.....((((............((((((((...))))))))(((((.(((((...))))).)))))))))....))))).))))... (-31.70 = -32.02 +   0.32)

alignment

secondary structure

dotplot

Window 8

Location	3,349,695 – 3,349,808
Length	113
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	90.96
Mean single sequence MFE	-36.80
Consensus MFE	-30.08
Energy contribution	-30.60
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-1.99
Structure conservation index	0.82
SVM decision value	1.47
SVM RNA-class probability	0.957213
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3349695 113 - 20766785
ACCUAAGGCUCGGCCACAAGAUUAAUUAGCAUUGCUGCGGUUGGGCCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUU
(((...(((((((((.((.(((........)))..)).)))))))))....(((-----(...))))....)))(((((((((...)))))))))((((.(((((...))))).)))) ( -38.20)
>DroSec_CAF1 10246 113 - 1
ACCUAAGGCUCGGCCACAAGAUUAAUUAGCAUUGCUGCGGUUGGGCCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUU
(((...(((((((((.((.(((........)))..)).)))))))))....(((-----(...))))....)))(((((((((...)))))))))((((.(((((...))))).)))) ( -38.20)
>DroSim_CAF1 3391 113 - 1
ACCUAAGGCUCGGCCACAAGAUUAAUGAGCAUUGCUGCGGUUGGACCAAUCGGA-----UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUU
.......((((.(((((...........(((....)))(((((((((....)).-----)))))))...)))))(((((((((...)))))))))))))...(((((.....))))). ( -38.70)
>DroEre_CAF1 1496 118 - 1
AUCUAAGGCUCCGCCACAAGAUUAAUUAGCAUUGCUGUGGUCGGGCCAAUCCGAACAAAUCCAAUCCAAUUGCAUUGCCAUGGCAGCCAUGGUAGGAGUGUCAAUCUAAUUGAGAUUU
......(((((.((((((.(((........)))..)))))).))))).........(((((((((...(((((((((((((((...))))))))...))).))))...)))).))))) ( -36.10)
>DroYak_CAF1 4876 113 - 1
GUCCAAGGCUCGGCCACAAGAUUAAUUAGCUUUGCUGCGGUUCAGCCAAUCCGA-----UUCAAUCCAAGUGCAUUGCCAUGGCAGCCGUGGCAGGACUGUCAAUCUAAUUGAGAUUU
(((((((((...)))...(((((...(((..((((..(((((..((((...(((-----(.((.......)).))))...)))))))))..))))..)))..)))))..))).))).. ( -32.80)
>consensus
ACCUAAGGCUCGGCCACAAGAUUAAUUAGCAUUGCUGCGGUUGGGCCAAUCGGA_____UCCAAUCCAAGUGGUUUGCCAUGGCAGCCAUGGCAGGAGUGUCAAUCUAAUUGAGAUUU
......(((((((((.((.(((........)))..)).)))))))))...........................(((((((((...)))))))))((((.(((((...))))).)))) (-30.08 = -30.60 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:26 2006