Locus 4147

Sequence ID	3R_DroMel_CAF1
Location	11,313,646 – 11,313,744
Length	98
Max. P	0.968235

overview

Window 3

Location	11,313,646 – 11,313,744
Length	98
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.29
Mean single sequence MFE	-30.27
Consensus MFE	-16.32
Energy contribution	-16.85
Covariance contribution	0.53
Combinations/Pair	1.22
Mean z-score	-1.97
Structure conservation index	0.54
SVM decision value	0.46
SVM RNA-class probability	0.746074
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11313646 98 + 27905053
GAUAUACAGCUGACCAAGGCGGAAAUGGCUGCCACCCAGAUACUAGUCACCACGCCGGAGAAAUGGGAUGUGGUAACCAGAAAGGGUAAU---AA--U-AAUAU------
.................(((((......)))))((((.(((....)))((((((((.........)).)))))).........))))...---..--.-.....------ ( -24.10)
>DroPse_CAF1 53206 99 + 1
GACAUGCAGCUGACCAAGGCGGAAAUGGCAGCCACCCAGAUAUUGGUAACCACGCCAGAGAAGUGGGAUGUGGUCACCAGAAAGGGUAAG---CA--UUAACUU------
...((((.((((.(((.........))))))).((((.....(((((.((((((((.........)).)))))).)))))...))))..)---))--)......------ ( -31.30)
>DroWil_CAF1 59716 101 + 1
GAUAUGCAGCUGACAAAAGCGGAGAUGGCGGCCACUCAAAUUCUCGUGACGACGCCGGAAAAGUGGGAUGUGGUCACACGAAAGGGUAGAUGCAA--U-AAAAA------
....(((((((......))).(((.(((...))))))....(((((((((.(((((.(.....).)).))).))))).(....).).))))))).--.-.....------ ( -26.60)
>DroMoj_CAF1 59596 106 + 1
GACAUGCAGCUGACCAAAGCAGAGAUGACGGCCACGCAGAUACUGGUCACCACGCCCGAAAAGUGGGAUGUUGUGACCAGAAAGGGUAAG---UCAAU-AAAUUGGCUCA
(((.(((.(((......))).....((.((....))))....((((((((.(((((((.....)))).))).)))))))).....))).)---))...-........... ( -32.20)
>DroAna_CAF1 49269 92 + 1
GACAUGCAGUUGACCAAAGCGGAGAUGACAGCCACCCAGAUUUUGGUUACCACCCCGGAGAAAUGGGAUGUGGUCACCCGAAAAGGUUAG---C---------U------
.......((((((((....(((.(.((((.((..((((..((((((........))))))...))))..)).))))))))....))))))---)---------)------ ( -29.90)
>DroPer_CAF1 53364 99 + 1
GACAUGCAGCUGACCAAGGCGGAAAUGGCAGCCACCCAGAUAUUGGUGACCACGCCAGAGAAGUGGGAUGUGGUCACCAGAAAGGGUAAG---CA--UUAACUU------
...((((.((((.(((.........))))))).((((.....((((((((((((((.........)).))))))))))))...))))..)---))--)......------ ( -37.50)
>consensus
GACAUGCAGCUGACCAAAGCGGAAAUGGCAGCCACCCAGAUACUGGUCACCACGCCGGAGAAGUGGGAUGUGGUCACCAGAAAGGGUAAG___CA__U_AAAUU______
..(((...(((......)))....)))......((((.....(((((.((((((((.........)).)))))).)))))...))))....................... (-16.32 = -16.85 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	11,313,646 – 11,313,744
Length	98
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.29
Mean single sequence MFE	-30.10
Consensus MFE	-20.28
Energy contribution	-20.23
Covariance contribution	-0.05
Combinations/Pair	1.43
Mean z-score	-2.38
Structure conservation index	0.67
SVM decision value	1.62
SVM RNA-class probability	0.968235
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11313646 98 - 27905053
------AUAUU-A--UU---AUUACCCUUUCUGGUUACCACAUCCCAUUUCUCCGGCGUGGUGACUAGUAUCUGGGUGGCAGCCAUUUCCGCCUUGGUCAGCUGUAUAUC
------.....-.--..---..(((((...(((((((((((...((........)).))))))))))).....)))))(((((.....((.....))...)))))..... ( -31.30)
>DroPse_CAF1 53206 99 - 1
------AAGUUAA--UG---CUUACCCUUUCUGGUGACCACAUCCCACUUCUCUGGCGUGGUUACCAAUAUCUGGGUGGCUGCCAUUUCCGCCUUGGUCAGCUGCAUGUC
------......(--((---(..((((....((((((((((...(((......))).))))))))))......))))((((((((.........))).)))))))))... ( -36.40)
>DroWil_CAF1 59716 101 - 1
------UUUUU-A--UUGCAUCUACCCUUUCGUGUGACCACAUCCCACUUUUCCGGCGUCGUCACGAGAAUUUGAGUGGCCGCCAUCUCCGCUUUUGUCAGCUGCAUAUC
------.....-.--.((((.((......(((((((((......((........)).)))).)))))((....((((((.........))))))...)))).)))).... ( -20.30)
>DroMoj_CAF1 59596 106 - 1
UGAGCCAAUUU-AUUGA---CUUACCCUUUCUGGUCACAACAUCCCACUUUUCGGGCGUGGUGACCAGUAUCUGCGUGGCCGUCAUCUCUGCUUUGGUCAGCUGCAUGUC
((((.(((...-.))).---))))......((((((((.((..(((.......))).)).))))))))....((((((((((............))))))..)))).... ( -28.40)
>DroAna_CAF1 49269 92 - 1
------A---------G---CUAACCUUUUCGGGUGACCACAUCCCAUUUCUCCGGGGUGGUAACCAAAAUCUGGGUGGCUGUCAUCUCCGCUUUGGUCAACUGCAUGUC
------.---------(---(..((((....))))(((((((((((........))))))....(((.....)))((((..(....).))))..)))))....))..... ( -25.60)
>DroPer_CAF1 53364 99 - 1
------AAGUUAA--UG---CUUACCCUUUCUGGUGACCACAUCCCACUUCUCUGGCGUGGUCACCAAUAUCUGGGUGGCUGCCAUUUCCGCCUUGGUCAGCUGCAUGUC
------......(--((---(..((((....((((((((((...(((......))).))))))))))......))))((((((((.........))).)))))))))... ( -38.60)
>consensus
______AAGUU_A__UG___CUUACCCUUUCUGGUGACCACAUCCCACUUCUCCGGCGUGGUCACCAAUAUCUGGGUGGCUGCCAUCUCCGCCUUGGUCAGCUGCAUGUC
......................(((((....((((((((((...((........)).))))))))))......)))))((.((.....((.....))...)).))..... (-20.28 = -20.23 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:23 2006