Locus 6482

Sequence ID	3R_DroMel_CAF1
Location	17,053,753 – 17,053,861
Length	108
Max. P	0.997150

overview

Window 8

Location	17,053,753 – 17,053,861
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	96.39
Mean single sequence MFE	-52.35
Consensus MFE	-50.10
Energy contribution	-50.34
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.86
Structure conservation index	0.96
SVM decision value	2.81
SVM RNA-class probability	0.997150
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17053753 108 + 27905053
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGCAGCACGCAGCGCACGAUUAUUACCCAAUCGAACACGGCGGCGGCGGCGUCGCAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(((((((((....((.(((.(.(..(((((.......)))))..).).)))))..)))))))))....))).).)))))))).)) ( -53.10)
>DroSec_CAF1 4161 108 + 1
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGCAGCACGCAGCGCACGAUUAUUACCCAAUCGAACACGGCGGCGACGGCGUCGCAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(((((((((....((.(((.(.(..(((((.......)))))..).).)))))..)))))))))....))).).)))))))).)) ( -54.20)
>DroEre_CAF1 4191 108 + 1
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGUAGUACGCAGCGCACGAUUAUUACUCAAUCGAACACGGCGGCGGCGGCGUCGCAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(((((((((....((.(((.(.(..(((((.......)))))..).).)))))..)))))))))....))).).)))))))).)) ( -50.40)
>DroYak_CAF1 4230 108 + 1
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGCAGCACGCAGCGCACGAUUAUUACCCAAUCAAACACGGCGGCGGCGGCGUCGCAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(((((((((....((.(((.......((((.......)))).......)))))..)))))))))....))).).)))))))).)) ( -50.14)
>DroAna_CAF1 3865 108 + 1
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGCAGCACGCAGCGCACGAUUAUUACCCAAUCGAGCCCAGCGGCGCCGGCGUCACAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(.((((((((...((.(((.(.((.(((((.......))))).)).).))))).)))))))).)....))).).)))))))).)) ( -53.90)
>consensus
AGCCGCAGCUGGUGCAGGUGCAGGCGGCGCCGGGCAGCACGCAGCGCACGAUUAUUACCCAAUCGAACACGGCGGCGGCGGCGUCGCAACAGCAGCCGCGCCAGCAGC
....((.((((((((.(.(((..(((((((((....((.(((......(((((.......)))))......)))))..)))))))))....))).).)))))))).)) (-50.10 = -50.34 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	17,053,753 – 17,053,861
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.39
Mean single sequence MFE	-55.12
Consensus MFE	-53.10
Energy contribution	-53.02
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-1.65
Structure conservation index	0.96
SVM decision value	2.22
SVM RNA-class probability	0.990503
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17053753 108 - 27905053
GCUGCUGGCGCGGCUGCUGUUGCGACGCCGCCGCCGCCGUGUUCGAUUGGGUAAUAAUCGUGCGCUGCGUGCUGCCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.((((((.(((((.((((.((((((.....)))))).)))).))).)).))..)))).)))..))).)))).))))).)).... ( -56.40)
>DroSec_CAF1 4161 108 - 1
GCUGCUGGCGCGGCUGCUGUUGCGACGCCGUCGCCGCCGUGUUCGAUUGGGUAAUAAUCGUGCGCUGCGUGCUGCCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.(((((..(((((.((((.((((((.....)))))).)))).))).))....))))).)))..))).)))).))))).)).... ( -55.60)
>DroEre_CAF1 4191 108 - 1
GCUGCUGGCGCGGCUGCUGUUGCGACGCCGCCGCCGCCGUGUUCGAUUGAGUAAUAAUCGUGCGCUGCGUACUACCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.(((((....(((.((((.((((((.....)))))).)))).))).......))))).)))..))).)))).))))).)).... ( -50.50)
>DroYak_CAF1 4230 108 - 1
GCUGCUGGCGCGGCUGCUGUUGCGACGCCGCCGCCGCCGUGUUUGAUUGGGUAAUAAUCGUGCGCUGCGUGCUGCCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.((((((.(((((.((((.((((((.....)))))).)))).))).)).))..)))).)))..))).)))).))))).)).... ( -54.80)
>DroAna_CAF1 3865 108 - 1
GCUGCUGGCGCGGCUGCUGUUGUGACGCCGGCGCCGCUGGGCUCGAUUGGGUAAUAAUCGUGCGCUGCGUGCUGCCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.((((((((((((.(.((.((((((.....)))))).)).).))).)).).)))))).)))..))).)))).))))).)).... ( -58.30)
>consensus
GCUGCUGGCGCGGCUGCUGUUGCGACGCCGCCGCCGCCGUGUUCGAUUGGGUAAUAAUCGUGCGCUGCGUGCUGCCCGGCGCCGCCUGCACCUGCACCAGCUGCGGCU
((.(((((.((((.(((....(((.(((((..(((((.((((.((((((.....)))))).)))).))).))....))))).)))..))).)))).))))).)).... (-53.10 = -53.02 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:28 2006