Locus 5500

Sequence ID	2R_DroMel_CAF1
Location	17,653,542 – 17,653,742
Length	200
Max. P	0.992460

overview

Window 8

Location	17,653,542 – 17,653,662
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.50
Mean single sequence MFE	-31.18
Consensus MFE	-31.16
Energy contribution	-30.68
Covariance contribution	-0.48
Combinations/Pair	1.10
Mean z-score	-1.57
Structure conservation index	1.00
SVM decision value	2.33
SVM RNA-class probability	0.992460
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17653542 120 + 20766785
GGAAAAUUGGGCCAACUUAAGCGGCGAUCUGGGGGAAGACUGGCCAAGAACGAUGACUAAGAAAUGUGUUAAUGAUAGCGAGUGGCGUAAUUAGCCAGAAAUAUUUCGUGUUGGCCAAAU
.........(((((((......(((.((((......))).).)))...............(((((((((((....))))...((((.......))))...)))))))..))))))).... ( -32.90)
>DroSec_CAF1 7175 120 + 1
GGAAAAUUGGGUCAACUUAAGCGGCGAUCUGGGGGAAGACUGGCCAAGAACGAUGACUAAGAAAUGUGUUAAUGAUAGCGAAUGGCGUAAUUAGCCAGAAAUAUUUCGCGUUGGCCAAAA
.........(((((((....(((((.((((......))).).)))...............(((((((((((....))))...((((.......))))...)))))))))))))))).... ( -30.90)
>DroSim_CAF1 13086 120 + 1
GGAAAAUUGGGUCAACUUAACUGGCGAUCUGGGGGAAGACUGGCCAAGAACAAUGACUAAGAAAUGUGUUAAUGAUAGCGAAUGGCGUAAUUAGCCAGAAAUAUUUCGCGUUGGCCAAAA
.........(((((((.....((((.((((......))).).))))....((.((((..(....)..)))).))...(((((((((.......)))).......)))))))))))).... ( -31.31)
>DroEre_CAF1 7360 120 + 1
GGAAAAUUGGGUCAACUUGAGCGGCGAUCUGGGGGAAGAGUGGCCAAGAACGAUGACUAAGAAAUGUGUUAAUGAUAGCGAGUGGUGUAAUUAGCCAGAAAUAUUUCUCGUUGGCCAAAA
.........(((((((......(((.((((......))).).)))..............((((((((((((....))))...((((.......))))...)))))))).))))))).... ( -28.30)
>DroYak_CAF1 18758 120 + 1
GGAAAAUUGGGUCAACUUGAGCGGCGAUCUGGGGGAAGACUGGCCAAGAACGAUGACUAAGAAAUGUGUUAAUGAUAGCGAGUGGCGUAAUUAGCCAGAAACAUUUCUCGUUGGCCAAAA
.........(((((((......(((.((((......))).).)))..............((((((((((((....))))...((((.......))))...)))))))).))))))).... ( -32.50)
>consensus
GGAAAAUUGGGUCAACUUAAGCGGCGAUCUGGGGGAAGACUGGCCAAGAACGAUGACUAAGAAAUGUGUUAAUGAUAGCGAGUGGCGUAAUUAGCCAGAAAUAUUUCGCGUUGGCCAAAA
.........(((((((......(((.((((......))).).)))...............(((((((((((....))))...((((.......))))...)))))))..))))))).... (-31.16 = -30.68 +  -0.48)

alignment

secondary structure

dotplot

Window 9

Location	17,653,582 – 17,653,702
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.50
Mean single sequence MFE	-31.58
Consensus MFE	-30.52
Energy contribution	-30.92
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-1.45
Structure conservation index	0.97
SVM decision value	1.51
SVM RNA-class probability	0.960077
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17653582 120 - 20766785
GCGAGCAUUUUGUGUGGCAUGCGACAGCAAAACGUUUUCGAUUUGGCCAACACGAAAUAUUUCUGGCUAAUUACGCCACUCGCUAUCAUUAACACAUUUCUUAGUCAUCGUUCUUGGCCA
(((((.((((((((((((...(((.(((.....))).))).....))).))))))))).....((((.......)))))))))....................((((.......)))).. ( -33.10)
>DroSec_CAF1 7215 120 - 1
GCGAGCAUUUUGUGUGGCAUGCGACAGCGGAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCAUUCGCUAUCAUUAACACAUUUCUUAGUCAUCGUUCUUGGCCA
(((((.((((((((((((..((((.((((...)))).))))....))).))))))))).....((((.......)))))))))....................((((.......)))).. ( -33.20)
>DroSim_CAF1 13126 120 - 1
GCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCAUUCGCUAUCAUUAACACAUUUCUUAGUCAUUGUUCUUGGCCA
(((((.((((((((((((..((((.((((...)))).))))....))).))))))))).....((((.......)))))))))....................((((.......)))).. ( -33.20)
>DroEre_CAF1 7400 120 - 1
GCGAGCAUUUUGUGUGGCAUGCGACAGCAAAACGUUUUCGUUUUGGCCAACGAGAAAUAUUUCUGGCUAAUUACACCACUCGCUAUCAUUAACACAUUUCUUAGUCAUCGUUCUUGGCCA
(((((......((((((...((((.(((.....))).)))).(((((((..((((....)))))))))))))))))..)))))....................((((.......)))).. ( -26.40)
>DroYak_CAF1 18798 120 - 1
GCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGAGAAAUGUUUCUGGCUAAUUACGCCACUCGCUAUCAUUAACACAUUUCUUAGUCAUCGUUCUUGGCCA
(((((((((((.((((((..((((.((((...)))).))))....))).))).))))))....((((.......)))))))))....................((((.......)))).. ( -32.00)
>consensus
GCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCACUCGCUAUCAUUAACACAUUUCUUAGUCAUCGUUCUUGGCCA
(((((.((((((((((((..((((.(((.....))).))))....))).))))))))).....((((.......)))))))))....................((((.......)))).. (-30.52 = -30.92 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	17,653,622 – 17,653,742
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.92
Mean single sequence MFE	-35.48
Consensus MFE	-31.82
Energy contribution	-32.34
Covariance contribution	0.52
Combinations/Pair	1.08
Mean z-score	-1.55
Structure conservation index	0.90
SVM decision value	1.36
SVM RNA-class probability	0.946123
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17653622 120 - 20766785
CAUGCAAUUUCCUGCUUCGGCUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCAAAACGUUUUCGAUUUGGCCAACACGAAAUAUUUCUGGCUAAUUACGCCACU
..((((.((((.((...((((.....))))...))))))))))...((((((((((((...(((.(((.....))).))).....))).))))))))).....((((.......)))).. ( -33.40)
>DroSec_CAF1 7255 120 - 1
CACGCAAUUUCCUGCCACGGCUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCGGAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCAUU
..((((.((((.((...((((.....))))...))))))))))...((((((((((((..((((.((((...)))).))))....))).))))))))).....((((.......)))).. ( -37.60)
>DroSim_CAF1 13166 120 - 1
CACGCAAUUUCCUGCCUCGGCUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCAUU
..((((.((((.((...((((.....))))...))))))))))...((((((((((((..((((.((((...)))).))))....))).))))))))).....((((.......)))).. ( -37.60)
>DroEre_CAF1 7440 120 - 1
CACGCAAUUUCCUGCCUCGAUUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCAAAACGUUUUCGUUUUGGCCAACGAGAAAUAUUUCUGGCUAAUUACACCACU
...(((......)))...........((((((.((((((((....)))))).)).)))).)).....(((((((....)))))))((((..((((....))))))))............. ( -28.10)
>DroYak_CAF1 18838 120 - 1
CACGCAAUUUCCUGCCGCGGCUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGAGAAAUGUUUCUGGCUAAUUACGCCACU
..((((.((((.((..(((((.....)))))..))))))))))((((((((.((((((..((((.((((...)))).))))....))).))).))))))))..((((.......)))).. ( -40.70)
>consensus
CACGCAAUUUCCUGCCUCGGCUUUCAGCUGCCCCAGAAAUGCGAGCAUUUUGUGUGGCAUGCGACAGCGAAACGUUUUCGUUUUGGCCAACGCGAAAUAUUUCUGGCUAAUUACGCCACU
..((((.((((.((...((((.....))))...))))))))))...((((((((((((..((((.(((.....))).))))....))).))))))))).....((((.......)))).. (-31.82 = -32.34 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:40 2006