Locus 193

Sequence ID	2R_DroMel_CAF1
Location	1,449,447 – 1,449,601
Length	154
Max. P	0.941492

overview

Window 1

Location	1,449,447 – 1,449,561
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.05
Mean single sequence MFE	-32.02
Consensus MFE	-29.90
Energy contribution	-29.74
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.93
SVM decision value	1.32
SVM RNA-class probability	0.941492
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1449447 114 + 20766785
UGUCUCUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGCCAGCCUCCCGUUUCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
.....((((((((((((.((((........))))..))))))((((.........))))------......))))))(((..((((((.....................))))))..))) ( -29.80)
>DroSec_CAF1 67609 114 + 1
UGUCUCUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGCCAGCCUCCCGUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
.....((((((((((((........))))))......((((.(((....).))...)))------).....))))))(((..((((((.....................))))))..))) ( -32.00)
>DroSim_CAF1 66485 114 + 1
UGUCUCUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGCCAGCCUCCCGUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
.....((((((((((((........))))))......((((.(((....).))...)))------).....))))))(((..((((((.....................))))))..))) ( -32.00)
>DroEre_CAF1 76995 120 + 1
UGUCUCUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGCCAGCCUCCCAUGCCUGGGCCCCGGCCCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
.....((((((((((((........))))))......((((.(...((((....))))..).)))).....))))))(((..((((((.....................))))))..))) ( -35.60)
>DroYak_CAF1 72569 113 + 1
UGUC-CUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGUCAGCCUCCCAUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
....-((((((.(((((.......(((((....))).)).))))).((((....)))).------......))))))(((..((((((.....................))))))..))) ( -30.70)
>consensus
UGUCUCUUUCAUGGCUGUUAAUUUCCAGCUAUUGUUCGGCCAGCCUCCCGUGCCUGGGC______CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACG
.....((((((((((((.((((........))))..))))))............((((.......))))..))))))(((..((((((.....................))))))..))) (-29.90 = -29.74 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	1,449,447 – 1,449,561
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.05
Mean single sequence MFE	-33.74
Consensus MFE	-28.30
Energy contribution	-28.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.84
SVM decision value	1.05
SVM RNA-class probability	0.906777
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1449447 114 - 20766785
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGG------GCCCAGAAACGGGAGGCUGGCCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAGAGACA
.(((.((((...(((((......)))))......)))).....((((((((((.(------(((.((...(....).))))))...)))).((((........))))..)))))).))). ( -31.90)
>DroSec_CAF1 67609 114 - 1
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGG------GCCCAGGCACGGGAGGCUGGCCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAGAGACA
.(((.((((...(((((......)))))......)))).....((((((((((.(------(((..(((.(....))))))))...)))).((((........))))..)))))).))). ( -33.70)
>DroSim_CAF1 66485 114 - 1
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGG------GCCCAGGCACGGGAGGCUGGCCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAGAGACA
.(((.((((...(((((......)))))......)))).....((((((((((.(------(((..(((.(....))))))))...)))).((((........))))..)))))).))). ( -33.70)
>DroEre_CAF1 76995 120 - 1
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGGGCCGGGGCCCAGGCAUGGGAGGCUGGCCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAGAGACA
.(((.((((...(((((......)))))......)))).....((((((((((.((((((..((((....))))...))))))...)))).((((........))))..)))))).))). ( -40.40)
>DroYak_CAF1 72569 113 - 1
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGG------GCCCAGGCAUGGGAGGCUGACCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAG-GACA
.(((.((((...(((((......)))))......)))).....((((((.((((.------.((((....)))).......))))......((((........))))..))))))-))). ( -29.00)
>consensus
CGUCAGGCACAGUGAUUGCUUAAAAUUAAAUUUAUGCCCAACGCUUUCAAUUGGG______GCCCAGGCACGGGAGGCUGGCCGAACAAUAGCUGGAAAUUAACAGCCAUGAAAGAGACA
.(((.((((...(((((......)))))......)))).....((((((((((.........(((......))).((....))...)))).((((........))))..)))))).))). (-28.30 = -28.30 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	1,449,487 – 1,449,601
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-29.94
Consensus MFE	-28.70
Energy contribution	-28.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.03
Structure conservation index	0.96
SVM decision value	0.01
SVM RNA-class probability	0.536189
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1449487 114 + 20766785
CAGCCUCCCGUUUCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCUCUUGAUGUCCACGUUGUUGUUUCACGCACACAUCAAU
.((((.((((....)))).------.............((..((((((.....................))))))..)))))).(((((((...(((.(......))))...))))))). ( -28.20)
>DroSec_CAF1 67649 114 + 1
CAGCCUCCCGUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCUCUUGAUGUCCACGUUGUUGUUUCACGCACACAUCAAU
.((((.((((....)))).------.............((..((((((.....................))))))..)))))).(((((((...(((.(......))))...))))))). ( -28.20)
>DroSim_CAF1 66525 114 + 1
CAGCCUCCCGUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCUCUUGAUGUCCACGUUGUUGUUUCACGCACACAUCAAU
.((((.((((....)))).------.............((..((((((.....................))))))..)))))).(((((((...(((.(......))))...))))))). ( -28.20)
>DroEre_CAF1 77035 120 + 1
CAGCCUCCCAUGCCUGGGCCCCGGCCCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCACUUGAUGUCCACGUUGUUGUUACACGCACACAUCAAU
..........((((.((((....))))...........((..((((((.....................))))))..)))))).(((((((...(((.((....)))))...))))))). ( -34.80)
>DroYak_CAF1 72608 114 + 1
CAGCCUCCCAUGCCUGGGC------CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCACUUGAUGUCCUCGUUGUUGUUACACGCUCACAUCAAA
..(((.((((....)))).------.............((..((((((.....................))))))..)))))..(((((((...(((.((....)))))...))))))). ( -30.30)
>consensus
CAGCCUCCCGUGCCUGGGC______CCCAAUUGAAAGCGUUGGGCAUAAAUUUAAUUUUAAGCAAUCACUGUGCCUGACGGCUCUUGAUGUCCACGUUGUUGUUUCACGCACACAUCAAU
..(((.........((((.......)))).........((..((((((.....................))))))..)))))..(((((((...(((.(......))))...))))))). (-28.70 = -28.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:00 2006