Locus 5426

Sequence ID	2R_DroMel_CAF1
Location	17,477,258 – 17,477,385
Length	127
Max. P	0.713916

overview

Window 4

Location	17,477,258 – 17,477,353
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	98.60
Mean single sequence MFE	-26.98
Consensus MFE	-25.97
Energy contribution	-25.83
Covariance contribution	-0.14
Combinations/Pair	1.03
Mean z-score	-0.86
Structure conservation index	0.96
SVM decision value	0.38
SVM RNA-class probability	0.713916
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17477258 95 + 20766785
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
......(((....((((((..((((((........))))))...(((..(((..((((((..(....)..))))))))).)))))))))..))). ( -27.80)
>DroSec_CAF1 5532 95 + 1
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
......(((....((((((..((((((........))))))...(((..(((..((((((..(....)..))))))))).)))))))))..))). ( -27.80)
>DroSim_CAF1 14099 95 + 1
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
......(((....((((((..((((((........))))))...(((..(((..((((((..(....)..))))))))).)))))))))..))). ( -27.80)
>DroEre_CAF1 5497 95 + 1
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
......(((....((((((..((((((........))))))...(((..(((..((((((..(....)..))))))))).)))))))))..))). ( -27.80)
>DroYak_CAF1 13447 95 + 1
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
......(((....((((((..((((((........))))))...(((..(((..((((((..(....)..))))))))).)))))))))..))). ( -27.80)
>DroAna_CAF1 5140 95 + 1
ACUUUAACUGUAAAAAGGUUUAUGGCAAACAGAAGCGCCAUCUAGUGCUCGUUAAGUGGCAACUGCAGACGCCGUUGCGUCGCGCAUUUCAAGUG
((((.((.(((....((((((.((.....)).))))((((..(((......)))..))))..))((.(((((....)))))))))).)).)))). ( -22.90)
>consensus
ACUUUAACUGUAAAAAUGUUUAUGGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUG
((((.((.(((......((((.((.....)).))))((((..((((....))))..))))....((.(((((....)))))))))).)).)))). (-25.97 = -25.83 +  -0.14)

alignment

secondary structure

dotplot

Window 5

Location	17,477,281 – 17,477,385
Length	104
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	96.60
Mean single sequence MFE	-33.52
Consensus MFE	-29.85
Energy contribution	-29.74
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-1.17
Structure conservation index	0.89
SVM decision value	0.03
SVM RNA-class probability	0.548290
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17477281 104 + 20766785
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUGCCCGGAAAACUGGGGAAAAUCCGC
((((........)))).....((((.(((..((((((..(....)..)))))))))..)))).......(((((....(.(((((....))))).)...))))) ( -37.50)
>DroSec_CAF1 5555 104 + 1
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUACCCGGAAAACUGGAGAAAAUCCGC
((((........)))).....((((.(((..((((((..(....)..)))))))))..)))).......(((((.......((((....))))......))))) ( -33.32)
>DroSim_CAF1 14122 104 + 1
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUGCCCGGAAAACUGGAGAAAAUCCGC
((((........)))).....((((.(((..((((((..(....)..)))))))))..)))).......(((((......(((((....)))).)....))))) ( -33.70)
>DroEre_CAF1 5520 104 + 1
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUGCCCGGAAAACUGAGCAAAAUCCGC
((((........)))).....((((.(((..((((((..(....)..)))))))))..)))).......(((((....(((.(((....))).)))...))))) ( -35.10)
>DroYak_CAF1 13470 104 + 1
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUGCCCGGAAAACUGAGGAAAAUCCGC
((((........)))).....((((.(((..((((((..(....)..)))))))))..)))).......(((((......(((((....))).))....))))) ( -33.70)
>DroAna_CAF1 5163 104 + 1
GGCAAACAGAAGCGCCAUCUAGUGCUCGUUAAGUGGCAACUGCAGACGCCGUUGCGUCGCGCAUUUCAAGUGGAAAACUGCCCGGAAAACUGUGAAAAAUCCGC
((((.......((((((..(((......)))..))))....((.(((((....))))))))).((((.....))))..))))((((.............)))). ( -27.82)
>consensus
GGCGAACAGAAGCGCCAUCUAGCGCUCGUUAAGUGGCAACUGCAGACGCCGCUGCGUCGCGCAUUUCAAGUGGAAAAAUGCCCGGAAAACUGGGGAAAAUCCGC
((((.......((((((..((((....))))..))))....((.(((((....))))))))).((((.....))))..))))((((.............)))). (-29.85 = -29.74 +  -0.11)

alignment

secondary structure

dotplot

Window 6

Location	17,477,281 – 17,477,385
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	96.60
Mean single sequence MFE	-33.43
Consensus MFE	-33.41
Energy contribution	-33.30
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-0.60
Structure conservation index	1.00
SVM decision value	0.07
SVM RNA-class probability	0.567795
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17477281 104 - 20766785
GCGGAUUUUCCCCAGUUUUCCGGGCAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((....(((((((((.......)))))))(((((((....))))).)).....))....)))(((((((....)))))))..)))))). ( -34.90)
>DroSec_CAF1 5555 104 - 1
GCGGAUUUUCUCCAGUUUUCCGGGUAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((....(((((((((.......)))))))(((((((....))))).)).....))....)))(((((((....)))))))..)))))). ( -32.90)
>DroSim_CAF1 14122 104 - 1
GCGGAUUUUCUCCAGUUUUCCGGGCAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((....(((((((((.......)))))))(((((((....))))).)).....))....)))(((((((....)))))))..)))))). ( -34.90)
>DroEre_CAF1 5520 104 - 1
GCGGAUUUUGCUCAGUUUUCCGGGCAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((....(((((((((.......)))))))(((((((....))))).)).....))....)))(((((((....)))))))..)))))). ( -34.90)
>DroYak_CAF1 13470 104 - 1
GCGGAUUUUCCUCAGUUUUCCGGGCAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((....(((((((((.......)))))))(((((((....))))).)).....))....)))(((((((....)))))))..)))))). ( -34.90)
>DroAna_CAF1 5163 104 - 1
GCGGAUUUUUCACAGUUUUCCGGGCAGUUUUCCACUUGAAAUGCGCGACGCAACGGCGUCUGCAGUUGCCACUUAACGAGCACUAGAUGGCGCUUCUGUUUGCC
((((((........(((.....(((((.((((.....))))((((.(((((....))))))))).)))))....)))((((.((....)).))))..)))))). ( -28.10)
>consensus
GCGGAUUUUCCCCAGUUUUCCGGGCAUUUUUCCACUUGAAAUGCGCGACGCAGCGGCGUCUGCAGUUGCCACUUAACGAGCGCUAGAUGGCGCUUCUGUUCGCC
((((((........(((.....((((..((((.....))))((((.(((((....)))))))))..))))....)))(((((((....)))))))..)))))). (-33.41 = -33.30 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:31 2006