Locus 8286

Sequence ID	3R_DroMel_CAF1
Location	22,147,672 – 22,147,789
Length	117
Max. P	0.976129

overview

Window 2

Location	22,147,672 – 22,147,789
Length	117
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.37
Mean single sequence MFE	-26.43
Consensus MFE	-24.56
Energy contribution	-24.37
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.23
Structure conservation index	0.93
SVM decision value	1.66
SVM RNA-class probability	0.970506
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22147672 117 + 27905053
UAAAA---AAUAAAAGAAACAAAGACACCGCACCGGUGCCGAGUAAUUGCCAAAUGUUUACGCACAUAUGUACGAUAUGUGAUAUUUGCAUAUAAACAGGCAUAUGUAGCCGCUUUUCAU
.....---...((((((((((....(((((...))))).(((....))).....)))))..((((((((((...(((((..(...)..)))))......)))))))).))..)))))... ( -25.00)
>DroSec_CAF1 78126 117 + 1
UAAAA---AAUAAAAGAAACAAAGACACCGCUCCGGUGCCGAGUAAUUGCCAAAUGUUUACGCACAUAUGUACGAUAUGUAAUAUUUGCAUAUAAACAGGCAUAUGUAGCCGCUUUUCAU
.....---...((((((((((....(((((...))))).(((....))).....)))))..((((((((((...(((((((.....)))))))......)))))))).))..)))))... ( -25.50)
>DroSim_CAF1 72611 120 + 1
AAAAAGAAUAUAAAAGAAACAAAGACACCGCUCCGGUGUCGAGUAAUUGCCAAAUGUUUACGCACAUAUGUACGAUAUGUAAUAUUUGCAUAUAAACAGGCAUAUGUAGCCGCUUUUCAU
.(((((..........(((((..(((((((...)))))))(.((....)))...)))))..((((((((((...(((((((.....)))))))......)))))))).))..)))))... ( -29.70)
>DroYak_CAF1 71000 111 + 1
---------AUAAAAGAAACAAAGACACCGCUCCGGUGCCGAGUAAUUGCCAAAUGUUUACGCACAUAUGUACGAUAUGUAAUAUUUGCAUAUAAACAGGCAUAUGUAGCCGCUUUUCAU
---------..((((((((((....(((((...))))).(((....))).....)))))..((((((((((...(((((((.....)))))))......)))))))).))..)))))... ( -25.50)
>consensus
UAAAA___AAUAAAAGAAACAAAGACACCGCUCCGGUGCCGAGUAAUUGCCAAAUGUUUACGCACAUAUGUACGAUAUGUAAUAUUUGCAUAUAAACAGGCAUAUGUAGCCGCUUUUCAU
...........((((((((((..(.(((((...))))).)(.((....)))...)))))..((((((((((...((((((((...))))))))......)))))))).))..)))))... (-24.56 = -24.37 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	22,147,672 – 22,147,789
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.37
Mean single sequence MFE	-28.95
Consensus MFE	-28.74
Energy contribution	-28.80
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.99
SVM decision value	1.76
SVM RNA-class probability	0.976129
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22147672 117 - 27905053
AUGAAAAGCGGCUACAUAUGCCUGUUUAUAUGCAAAUAUCACAUAUCGUACAUAUGUGCGUAAACAUUUGGCAAUUACUCGGCACCGGUGCGGUGUCUUUGUUUCUUUUAUU---UUUUA
...(((((..((......((((((((((((((.........)))).(((((....)))))))))))...)))).......(((((((...)))))))...))..)))))...---..... ( -27.60)
>DroSec_CAF1 78126 117 - 1
AUGAAAAGCGGCUACAUAUGCCUGUUUAUAUGCAAAUAUUACAUAUCGUACAUAUGUGCGUAAACAUUUGGCAAUUACUCGGCACCGGAGCGGUGUCUUUGUUUCUUUUAUU---UUUUA
...(((((..((......(((((((((((..(((.(((((((.....))).)))).))))))))))...)))).......(((((((...)))))))...))..)))))...---..... ( -29.20)
>DroSim_CAF1 72611 120 - 1
AUGAAAAGCGGCUACAUAUGCCUGUUUAUAUGCAAAUAUUACAUAUCGUACAUAUGUGCGUAAACAUUUGGCAAUUACUCGACACCGGAGCGGUGUCUUUGUUUCUUUUAUAUUCUUUUU
...(((((..((......(((((((((((..(((.(((((((.....))).)))).))))))))))...)))).......(((((((...)))))))...))..)))))........... ( -29.80)
>DroYak_CAF1 71000 111 - 1
AUGAAAAGCGGCUACAUAUGCCUGUUUAUAUGCAAAUAUUACAUAUCGUACAUAUGUGCGUAAACAUUUGGCAAUUACUCGGCACCGGAGCGGUGUCUUUGUUUCUUUUAU---------
...(((((..((......(((((((((((..(((.(((((((.....))).)))).))))))))))...)))).......(((((((...)))))))...))..)))))..--------- ( -29.20)
>consensus
AUGAAAAGCGGCUACAUAUGCCUGUUUAUAUGCAAAUAUUACAUAUCGUACAUAUGUGCGUAAACAUUUGGCAAUUACUCGGCACCGGAGCGGUGUCUUUGUUUCUUUUAUU___UUUUA
...(((((..((......(((((((((((..(((.(((((((.....))).)))).))))))))))...)))).......(((((((...)))))))...))..)))))........... (-28.74 = -28.80 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:56 2006