Locus 1615

Sequence ID	2R_DroMel_CAF1
Location	6,048,929 – 6,049,091
Length	162
Max. P	0.842309

overview

Window 4

Location	6,048,929 – 6,049,024
Length	95
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	79.51
Mean single sequence MFE	-17.07
Consensus MFE	-15.06
Energy contribution	-14.70
Covariance contribution	-0.36
Combinations/Pair	1.11
Mean z-score	-1.12
Structure conservation index	0.88
SVM decision value	0.20
SVM RNA-class probability	0.632332
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6048929 95 - 20766785
AUAUUAAAACAA--GUUGAGUUUUUCGCUAACAACGUUUCGUAAAAUGAAAAUUUUGAACGUAGUUUGAUAGUAGAUCUCAACACAAGGAA-AUAUG-------A
............--((((((...((..(((((.((((((...(((((....))))))))))).))....)))..)).))))))........-.....-------. ( -18.20)
>DroPse_CAF1 66906 92 - 1
ACACCAAAAAUGCAGUUGAGUUUUUCGCUAACAACGUUUUGUAUAAUGA--AAUUUGAACGUAGUUUGAUAGUAGAUCUCAACACAGUAU-----------UCUC
........(((((.((((((...((..(((((.((((((...((.....--.))..)))))).))....)))..)).))))))...))))-----------)... ( -16.00)
>DroEre_CAF1 68076 97 - 1
AUAUUAAAACAAAUGUUGAGUUUUUCGCUAACAACGUUUCGUAAAAUGAUCAUUUUGAACGUAGUUUGAUAGUAGAUCUCAACACAAGAAA-AUAUU-------A
.............(((((((...((..(((((.((((((...(((((....))))))))))).))....)))..)).))))))).......-.....-------. ( -17.00)
>DroYak_CAF1 66881 96 - 1
AGAUUAAAACAAAAGUUGAGUUUUUCGCUAACAACGUUUCGUAA-AUGAAAAUUUUGAACGUAGUUUGAUAGUAGAUCUCAGCACAAGGAA-AUAUU-------A
..............((((((...((..(((((.((((((...((-((....)))).)))))).))....)))..)).))))))........-.....-------. ( -18.10)
>DroAna_CAF1 70307 104 - 1
AAACUAAUCCA-CAGCUGAGUUUUUCGCUAACAACGUUUCUUAAAAUGAUUAAUUUGAACGUAGUUUGAUAGUAGAUCUCAGCACAGUCACUAUAUCAUCUUUUA
...........-..((((((...((..(((((.((((((....((((.....)))))))))).))....)))..)).))))))...................... ( -17.80)
>DroPer_CAF1 66603 92 - 1
ACACCAAAAAUGCAGUUGAGUUUUUCGCUAACAACGUUUCGUAAAAUGA--AAUUUGAACGUAGUUUGAUAGUAGAUCUCAACACAGUAU-----------UCUC
........(((((.((((((...((..(((.....(((((((...))))--)))(..(((...)))..))))..)).))))))...))))-----------)... ( -15.30)
>consensus
ACACUAAAACAACAGUUGAGUUUUUCGCUAACAACGUUUCGUAAAAUGA__AAUUUGAACGUAGUUUGAUAGUAGAUCUCAACACAAGAAA_AUAU________A
..............((((((...((..(((((.((((((.................)))))).))....)))..)).))))))...................... (-15.06 = -14.70 +  -0.36)

alignment

secondary structure

dotplot

Window 5

Location	6,048,993 – 6,049,091
Length	98
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.28
Mean single sequence MFE	-20.03
Consensus MFE	-13.44
Energy contribution	-13.55
Covariance contribution	0.11
Combinations/Pair	1.17
Mean z-score	-1.93
Structure conservation index	0.67
SVM decision value	0.76
SVM RNA-class probability	0.842309
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6048993 98 - 20766785
AUUAAAGCAGCAACCCAAUC-----AAAUUGCGAAAAAUAUAACAUUAGUUUUUCGUACUACAG--CGGUUGCAAUAUUAAAACAA--GUUGAGUUUUUCGCUAACA
.....(((.((((((.....-----....((((((((((.........))))))))))......--.))))))......(((((..--.....)))))..))).... ( -20.19)
>DroPse_CAF1 66965 101 - 1
--CCAUUCAGCAUCUCGUUCAUCGUAAAGUAUGAAAAUUAGUACA----CUUUCCAUACGACAGAACGGUUGCAACACCAAAAAUGCAGUUGAGUUUUUCGCUAACA
--..(((((((...((((((.(((((((((.((........)).)----)))....)))))..)))))).((((..........)))))))))))............ ( -18.30)
>DroSec_CAF1 67128 98 - 1
GUAAAAGCAGCAACCCAAUC-----AAAUUGCGAAAAAUAUAACAUUAGUUUUUCGUACUACAG--CGGUUGCAAUAUUAACCCAA--GUUGAGUUUUUCGCUAACA
((((((((.((((((.....-----....((((((((((.........))))))))))......--.))))))....(((((....--))))))))))).))..... ( -21.89)
>DroSim_CAF1 70382 97 - 1
GUAAAAGCAGCAACCUAAUC-----AAAUUGCGAAAAAUAUAACAUUAGUU-UUCGUACUACAG--CGGUUGCAAUAUUAACCCAA--GUUGAGUUUUUCGCUAACA
((((((((.((((((.....-----....((((((((.((......)).))-))))))......--.))))))....(((((....--))))))))))).))..... ( -20.79)
>DroEre_CAF1 68140 97 - 1
GUAAAA---GCAACCCAAUC-----AAAUUGCGGAAAAUAUAACAUCAGUUUUUCGUACUACAG--UGGUUGCAAUAUUAAAACAAAUGUUGAGUUUUUCGCUAACA
((((((---((....(((((-----(...((((((((((.........))))))))))......--))))))(((((((......))))))).)))))).))..... ( -19.20)
>DroYak_CAF1 66944 97 - 1
GUAAGA---GCAACCCAAUC-----AAAUUGCGGAAAAUAUACCAUCAGUUUUUCGUACUACAG--CGGUUGCGAGAUUAAAACAAAAGUUGAGUUUUUCGCUAACA
((.((.---((((((.....-----....((((((((((.........))))))))))......--.))))))((((....(((....))).....)))).)).)). ( -19.79)
>consensus
GUAAAAGCAGCAACCCAAUC_____AAAUUGCGAAAAAUAUAACAUUAGUUUUUCGUACUACAG__CGGUUGCAAUAUUAAAACAA__GUUGAGUUUUUCGCUAACA
.........((((((..............((((((((((.........))))))))))(....)...))))))...............(((.(((.....)))))). (-13.44 = -13.55 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:55 2006