Locus 4112

Sequence ID	3R_DroMel_CAF1
Location	11,221,272 – 11,221,416
Length	144
Max. P	0.658402

overview

Window 8

Location	11,221,272 – 11,221,383
Length	111
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	83.77
Mean single sequence MFE	-29.95
Consensus MFE	-21.10
Energy contribution	-21.85
Covariance contribution	0.75
Combinations/Pair	1.22
Mean z-score	-2.27
Structure conservation index	0.70
SVM decision value	0.26
SVM RNA-class probability	0.658402
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11221272 111 - 27905053
AACGAAAUAUAGCCCUAUUUUAGCCCCGA---UUUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGUUCAUUACUUGCAUUUGCACAAGCUUUGGUAUGCAGUUAA
..(((((...(((((......(((((.(.---...))))))....))))).(((((((----...)))))))))))).....(((.((((((..((....))......)))))).))) ( -31.10)
>DroSec_CAF1 23147 111 - 1
AACGAAAUAUAGCCCUAUUUCAGCCCCGA---UAUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGUACAUUACUUGCAUUUGCACAAGCUUUGGUAUGCAGUUAA
..(((((...(((((......(((((.(.---...))))))....))))).(((((((----...)))))))))))).....(((.((((((..((....))......)))))).))) ( -30.40)
>DroSim_CAF1 23767 111 - 1
AACGAAAUAUAGCCCUAUUUUAGCCCCGA---UAUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGUACAUUACUUGCAUUUGCACAAGCUUUGGUAUGCAGUUAA
..(((((...(((((......(((((.(.---...))))))....))))).(((((((----...)))))))))))).....(((.((((((..((....))......)))))).))) ( -31.10)
>DroEre_CAF1 28590 115 - 1
AACGAAAUAUAGCCCUAUUUGAACCCCGC---UUUCGGACUUCUUGGGUUCUCUGAAUUACUUAUGUUCAGAUAUCGGUUCAUUUCUUGCAUUUGCACAAGCUUUUGUAUGCAGUUAA
((((((((..((((......((((((...---.............))))))(((((((.......)))))))....)))).))))).(((((..((....))......)))))))).. ( -24.99)
>DroYak_CAF1 24087 115 - 1
AACGAAAUAUAGCCCUAUUCGAACCCCGA---UUUCGGACUUCUUGGGUUCUCUGAAUUACUUAUGUUCAGAUUUCGGUUCAUUUCUUGCAUUUGCACAAGCUUUUGUAUGCAGUUGA
((((((((..((((......((((((.((---.........))..))))))(((((((.......)))))))....)))).))))).(((((..((....))......)))))))).. ( -26.40)
>DroAna_CAF1 23739 115 - 1
UACGAAUUGUUGCCCUAUU-CAGCUCCAAAGUUUUGGGAGCUCUGGGCGUUUCUGAAUUGC--AUAUUCAGAGUUUUGUUCUUUAGUGGCAAUUGCAUAAGCAUUCGUAUGCAUUGUA
((((((..(((((((((..-.((((((.........))))))..(((((.((((((((...--..))))))))...)))))..))).))))))(((....)))))))))......... ( -35.70)
>consensus
AACGAAAUAUAGCCCUAUUUCAGCCCCGA___UUUCGGACUUCUUGGGCUCUCUGAAU____UAUGUUCAGAUUUCGGUUCAUUACUUGCAUUUGCACAAGCUUUGGUAUGCAGUUAA
..(((((...(((((......((.(((((.....))))).))...))))).(((((((.......)))))))))))).........((((((..((....))......)))))).... (-21.10 = -21.85 +   0.75)

alignment

secondary structure

dotplot

Window 9

Location	11,221,311 – 11,221,416
Length	105
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	83.89
Mean single sequence MFE	-26.83
Consensus MFE	-16.74
Energy contribution	-16.93
Covariance contribution	0.20
Combinations/Pair	1.16
Mean z-score	-2.89
Structure conservation index	0.62
SVM decision value	0.23
SVM RNA-class probability	0.643429
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11221311 105 + 27905053
ACCGAAAUCUGAACAUA----AUUCAGAGAGCCCAAGAAGCCCGAAA---UCGGGGCUAAAAUAGGGCUAUAUUUCGUUAGCCA-AACGAA--GAAGGUAAUAUUUAAU----UCAAUU
(((....((((((....----.)))))).(((((....(((((....---...)))))......)))))...(((((((.....-))))))--)..)))..........----...... ( -28.80)
>DroSec_CAF1 23186 105 + 1
ACCGAAAUCUGAACAUA----AUUCAGAGAGCCCAAGAAGCCCGAUA---UCGGGGCUGAAAUAGGGCUAUAUUUCGUUAGCCA-AACGAA--GAAGGUAAUAUUUAAU----UCAAUU
(((....((((((....----.)))))).(((((....(((((....---...)))))......)))))...(((((((.....-))))))--)..)))..........----...... ( -29.90)
>DroSim_CAF1 23806 105 + 1
ACCGAAAUCUGAACAUA----AUUCAGAGAGCCCAAGAAGCCCGAUA---UCGGGGCUAAAAUAGGGCUAUAUUUCGUUAGCCA-AACGAA--GAAGGUAAUAUUUAAU----UCAAUU
(((....((((((....----.)))))).(((((....(((((....---...)))))......)))))...(((((((.....-))))))--)..)))..........----...... ( -28.80)
>DroEre_CAF1 28629 109 + 1
ACCGAUAUCUGAACAUAAGUAAUUCAGAGAACCCAAGAAGUCCGAAA---GCGGGGUUCAAAUAGGGCUAUAUUUCGUUAGCCA-AACGAA--GAAGGUAAUAUUUAAU----UCAAUU
(((....((((((.........))))))((((((.....((......---)).))))))......(((((........))))).-......--...)))..........----...... ( -23.60)
>DroYak_CAF1 24126 110 + 1
ACCGAAAUCUGAACAUAAGUAAUUCAGAGAACCCAAGAAGUCCGAAA---UCGGGGUUCGAAUAGGGCUAUAUUUCGUUAGCCAAAACGAA--GAAGGUAAUAUUUAAU----UCAAUU
...(((.((((((.........))))))..(((...(((.((((...---.)))).)))......(((((........)))))........--...))).........)----)).... ( -24.50)
>DroAna_CAF1 23778 115 + 1
ACAAAACUCUGAAUAU--GCAAUUCAGAAACGCCCAGAGCUCCCAAAACUUUGGAGCUG-AAUAGGGCAACAAUUCGUAAGACA-AGCGAAAAAAAGGUAAUAUUGAAUAAACACACUU
.(((...(((((((..--...))))))).((((((..((((((.........)))))).-....)))).....(((((......-.)))))......))....)))............. ( -25.40)
>consensus
ACCGAAAUCUGAACAUA____AUUCAGAGAGCCCAAGAAGCCCGAAA___UCGGGGCUAAAAUAGGGCUAUAUUUCGUUAGCCA_AACGAA__GAAGGUAAUAUUUAAU____UCAAUU
.......((((((.........))))))............(((((.....)))))....(((((..(((....((((((......)))))).....)))..)))))............. (-16.74 = -16.93 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	11,221,311 – 11,221,416
Length	105
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	83.89
Mean single sequence MFE	-25.57
Consensus MFE	-17.92
Energy contribution	-18.75
Covariance contribution	0.83
Combinations/Pair	1.18
Mean z-score	-2.09
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.591170
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11221311 105 - 27905053
AAUUGA----AUUAAAUAUUACCUUC--UUCGUU-UGGCUAACGAAAUAUAGCCCUAUUUUAGCCCCGA---UUUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGU
......----..........(((...--((((((-.....))))))....(((((......(((((.(.---...))))))....))))).(((((((----...)))))))....))) ( -27.70)
>DroSec_CAF1 23186 105 - 1
AAUUGA----AUUAAAUAUUACCUUC--UUCGUU-UGGCUAACGAAAUAUAGCCCUAUUUCAGCCCCGA---UAUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGU
......----..........(((...--((((((-.....))))))....(((((......(((((.(.---...))))))....))))).(((((((----...)))))))....))) ( -27.00)
>DroSim_CAF1 23806 105 - 1
AAUUGA----AUUAAAUAUUACCUUC--UUCGUU-UGGCUAACGAAAUAUAGCCCUAUUUUAGCCCCGA---UAUCGGGCUUCUUGGGCUCUCUGAAU----UAUGUUCAGAUUUCGGU
......----..........(((...--((((((-.....))))))....(((((......(((((.(.---...))))))....))))).(((((((----...)))))))....))) ( -27.70)
>DroEre_CAF1 28629 109 - 1
AAUUGA----AUUAAAUAUUACCUUC--UUCGUU-UGGCUAACGAAAUAUAGCCCUAUUUGAACCCCGC---UUUCGGACUUCUUGGGUUCUCUGAAUUACUUAUGUUCAGAUAUCGGU
......----..........(((...--((((((-.....))))))....(((((.....(((..(((.---...)))..)))..))))).(((((((.......)))))))....))) ( -22.10)
>DroYak_CAF1 24126 110 - 1
AAUUGA----AUUAAAUAUUACCUUC--UUCGUUUUGGCUAACGAAAUAUAGCCCUAUUCGAACCCCGA---UUUCGGACUUCUUGGGUUCUCUGAAUUACUUAUGUUCAGAUUUCGGU
......----................--((((..(.(((((........)))))..)..))))..((((---....(((((.....)))))(((((((.......)))))))..)))). ( -23.20)
>DroAna_CAF1 23778 115 - 1
AAGUGUGUUUAUUCAAUAUUACCUUUUUUUCGCU-UGUCUUACGAAUUGUUGCCCUAUU-CAGCUCCAAAGUUUUGGGAGCUCUGGGCGUUUCUGAAUUGC--AUAUUCAGAGUUUUGU
(((((.........................))))-).....(((((.....((((....-.((((((.........))))))..))))..((((((((...--..)))))))).))))) ( -25.71)
>consensus
AAUUGA____AUUAAAUAUUACCUUC__UUCGUU_UGGCUAACGAAAUAUAGCCCUAUUUCAGCCCCGA___UUUCGGACUUCUUGGGCUCUCUGAAU____UAUGUUCAGAUUUCGGU
....................(((.....((((((......))))))....(((((......((.(((((.....))))).))...))))).(((((((.......)))))))....))) (-17.92 = -18.75 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:30 2006