Locus 1976

Sequence ID	2R_DroMel_CAF1
Location	7,466,681 – 7,466,811
Length	130
Max. P	0.876800

overview

Window 0

Location	7,466,681 – 7,466,788
Length	107
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	74.45
Mean single sequence MFE	-25.93
Consensus MFE	-11.00
Energy contribution	-11.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.42
SVM decision value	0.80
SVM RNA-class probability	0.853420
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7466681 107 - 20766785
UUGGCCACACUCAGCUGA----CUUACUGCCUUGGCGGCCUGUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAAC-------
(((((((......(((.(----(...((((....))))...)).)))..........((((((.(((...))).))(((....)))......))))..)))))))......------- ( -29.90)
>DroVir_CAF1 89488 105 - 1
--GUUUUUGUUGCGGCA--------ACUUAAA--AAUGGCCAUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAACAA-CAAC
--(((.((((((.(...--------.).....--..((((((...(((.............((.(((...))).))(((....)))......)))...))))))...))))))-.))) ( -26.50)
>DroGri_CAF1 84198 105 - 1
--GUUGUUGUUGAGGCA--------ACUUCCA--AAUGGCGAUAGCAAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAACAG-CACC
--((((((((.(((...--------.)))(((--(...((....))...........((((((.(((...))).))(((....)))......)))).)))).....)))))))-)... ( -27.70)
>DroMoj_CAF1 107155 99 - 1
--------GUUGCGGCA--------ACUGCCA--AAUGGCCAUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAACAA-CAGC
--------((((.(((.--------...))).--..((((((...(((.............((.(((...))).))(((....)))......)))...))))))...))))..-.... ( -27.90)
>DroAna_CAF1 80051 88 - 1
-----------------------UUACAGCCCGGUCUCCUCGUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAAC-------
-----------------------.....(.(((((((......))))..........((((((.(((...))).))(((....)))......))))..))).)........------- ( -15.50)
>DroPer_CAF1 78028 112 - 1
UUCGCC---UUUAGCUGUGCUUUUUACUGCCUUG---GCCCAUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAAAAAACACC
.((((.---....(.(((((((((((.(((((..---......)))))...)))))).))))).).....))))(((((.....(((.....)))....))))).............. ( -28.10)
>consensus
__G_____GUUGAGGCA________ACUGCCA__AAUGCCCAUAGGCAAAUUAAAAAUGCACAACGCAAUGCGAUGGCCUAACGGUAAUUAAUGCAAUUGGUCAAUACAACAA_CA_C
.........................................................((((((.(((...))).))(((....)))......))))...................... (-11.00 = -11.00 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	7,466,714 – 7,466,811
Length	97
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.50
Mean single sequence MFE	-33.45
Consensus MFE	-21.53
Energy contribution	-21.92
Covariance contribution	0.39
Combinations/Pair	1.08
Mean z-score	-2.01
Structure conservation index	0.64
SVM decision value	0.90
SVM RNA-class probability	0.876800
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7466714 97 + 20766785
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUACAGGCCGCCAAGGCAGUAAG----UCAGCUGAGUGUGGCCAAAAGCGUAAGGCAAAUGGCCAACG----------------
(((((.((.(((((((..(((.........))).....((((((.....((((...----...))))...))))))...))))))).))..))))).....---------------- ( -32.10)
>DroPse_CAF1 108201 111 + 1
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUAUGGGC---CAAGGCAGUAAAAAGCACAGCUAAA---GGCGAACAGCUCGCAGCAAAUGGCCAACACAGCCAACAGCCAACA
......((.(((((((((((.((((((...(((((......---..))))).)))))))))))))....---.((((.....)))).)))).((((.......))))...))..... ( -35.80)
>DroSim_CAF1 75474 97 + 1
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUACGGGCCGCCAAGGCAGUAAG----UCAGCUGAGUGUGGCCAAAAGCGUAAGGCAAAUGCCCAACG----------------
((....))....(((((.(((((.......((((((((((((((.....((((...----...))))...)))))).....))).)))))))))).)))))---------------- ( -32.11)
>DroEre_CAF1 82796 97 + 1
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUACGGGCCUCCAAGGCAGUAAG----UCAGCUGAGUCUGGCCAAAAGCGUAAGGCAAAUGGCCAACG----------------
(((...((((......)))).......(((((((((((((((.......((((...----...)))).....)))).....))).))))))))))).....---------------- ( -31.20)
>DroYak_CAF1 81445 97 + 1
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUACGGGCCGCCAAGGCAGCAAG----UCAGCUGAGUCUGGCCAAAAGCGUAAGGCAAAUGGCCAACG----------------
(((((....((((.((((((...........(((....))).((((...((((...----...))))....)))).....)))))).))))))))).....---------------- ( -33.70)
>DroPer_CAF1 78068 111 + 1
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUAUGGGC---CAAGGCAGUAAAAAGCACAGCUAAA---GGCGAACAGCUCGCAGCAAAUGGCCAACACAGCCAACAGCCAACA
......((.(((((((((((.((((((...(((((......---..))))).)))))))))))))....---.((((.....)))).)))).((((.......))))...))..... ( -35.80)
>consensus
GCCAUCGCAUUGCGUUGUGCAUUUUUAAUUUGCCUACGGGCCGCCAAGGCAGUAAG____UCAGCUGAGU_UGGCCAAAAGCGUAAGGCAAAUGGCCAACG________________
(((((....((((.((((((.........((((((...(.....).))))))...........(((......))).....)))))).)))))))))..................... (-21.53 = -21.92 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:54 2006