Locus 1636

Sequence ID	2L_DroMel_CAF1
Location	4,399,507 – 4,399,749
Length	242
Max. P	0.940330

overview

Window 4

Location	4,399,507 – 4,399,620
Length	113
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	77.60
Mean single sequence MFE	-40.89
Consensus MFE	-20.96
Energy contribution	-23.02
Covariance contribution	2.06
Combinations/Pair	1.23
Mean z-score	-2.45
Structure conservation index	0.51
SVM decision value	1.31
SVM RNA-class probability	0.940330
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4399507 113 + 22407834
GCUGCCCAACCAGUGGUUGGCCUUGUUAAUCUUAUUUGGUGGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCGAAAUUCCAGGAGAACAAGUAGGUGCUA--GCUG-ACCAAU
((((......))))(((..((...((....((((((((.((.((((((((((((......).))))))))))).))...(((.....))))))))))).))..--))..-)))... ( -40.60)
>DroVir_CAF1 6271 116 + 1
AUUGCCACAGCUCUGGCUGCCUAUUCUCGUGCUAUUUGGCAGCAGCUUGCUGAGUCUCAUCAUCAGCGAGCUGGCCAAGCUGCAGGAGAACAAGUAAGUGCAGUUACCAAAUAUUU
((((((.((((....))))....(((((.(((..((((((..(((((((((((.........)))))))))))))))))..))).))))).......).)))))............ ( -46.90)
>DroSim_CAF1 5165 113 + 1
GCUGCCCAACCAGUGGAUUGCCUUGUUGAUCUUAUUUGGUGGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAUGUGCUA--GCUG-ACCAUU
((((((..(((((.(((((........)))))...))))))))))).....(((....)))((((((.(((..((...((((.....))))..))....))).--))))-)).... ( -39.40)
>DroEre_CAF1 5170 113 + 1
GCUGCCCAACCAAUGGGUGGCCUUGUUGAUCUUAUUUGGUGGCAGCUUUCUGAGUAUGCUUGUUAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUUACA--UUGG-ACCUUU
((..((((.....))))..))((((((..((((......((.((((((.((((.((....)))))).)))))).)).......)))).)))))).(((((...--...)-)))).. ( -36.82)
>DroYak_CAF1 5171 113 + 1
GCUACCCAACCAGUGGGUGGCCUUGUUGAUCUUAUUUGGUGGCAGCUUGCUAAGUAUGCUUGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUGACA--GCUG-ACCAUA
((((((((.....))))))))...((((..(((((((..((.((((((((((((....)))...))))))))).))..((((.....)))))))))))...))--))..-...... ( -41.30)
>DroAna_CAF1 7768 111 + 1
GCUGCCCAAAGUGUGGGUGGCCAUGUUAGUCCUAUUUGGCGGCAGUCUUCUGAGUAUGAUUGCCAGUGAGCUGGCCAAGUUCCAGGAGAAUAAGUGAGUGUUA--U-UC-ACAAU-
((..((((.....))))..))..((((..((((((((((((((((((..........)))))))((....)).)))))))...)))).)))).((((((...)--)-))-))...- ( -40.30)
>consensus
GCUGCCCAACCAGUGGGUGGCCUUGUUGAUCUUAUUUGGUGGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUGCUA__GCUG_ACCAUU
((((.(((.....))).))))((((((..((((......((.(((((((((((.........))))))))))).)).......)))).))))))...................... (-20.96 = -23.02 +   2.06)

alignment

secondary structure

dotplot

Window 5

Location	4,399,547 – 4,399,643
Length	96
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.10
Mean single sequence MFE	-28.66
Consensus MFE	-17.43
Energy contribution	-18.10
Covariance contribution	0.67
Combinations/Pair	1.12
Mean z-score	-1.70
Structure conservation index	0.61
SVM decision value	0.67
SVM RNA-class probability	0.818528
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4399547 96 + 22407834
GGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCGAAAUUCCAGGAGAACAAGUAGGUGCUA--GCUG-ACCAAUGUUCUAUG-----AUAAU-AUUAAAUGUU
(.((((((((((((......).))))))))))).).......((..((((((.((.(((....--))).-))...)))))).))-----.....-.......... ( -28.80)
>DroVir_CAF1 6311 104 + 1
AGCAGCUUGCUGAGUCUCAUCAUCAGCGAGCUGGCCAAGCUGCAGGAGAACAAGUAAGUGCAGUUACCAAAUAUUUGGUUGAGUUAUAU-AUUUAAUCAAUAUUU
..(((((((((((.........)))))))))))....(((((((..............)))))))...(((((((.((((((((.....-))))))))))))))) ( -32.84)
>DroSec_CAF1 5209 96 + 1
GGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAUGUGCUA--GCUG-ACCAUUGUUGUAUG-----CCUUU-AUUAAUUGUU
(((((((.((.(((....))))).))).((((((((..((((.....)))).......)))))--))).-............))-----))...-.......... ( -27.10)
>DroSim_CAF1 5205 96 + 1
GGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAUGUGCUA--GCUG-ACCAUUGUUGUAUG-----CCUUU-AUUAAUUGUU
(((((((.((.(((....))))).))).((((((((..((((.....)))).......)))))--))).-............))-----))...-.......... ( -27.10)
>DroEre_CAF1 5210 96 + 1
GGCAGCUUUCUGAGUAUGCUUGUUAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUUACA--UUGG-ACCUUUUUUGAGUU-----CCUCU-AUUAAGUGUA
((.((((((.(.(((.((((....)))).))).).))))))))(((((..((((.(((((...--...)-))))..))))..))-----)))..-.......... ( -26.70)
>DroYak_CAF1 5211 96 + 1
GGCAGCUUGCUAAGUAUGCUUGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUGACA--GCUG-ACCAUAGUGGUAAU-----CCUCU-ACUAAUUGUA
(((((((((((........(((((((....))))))).((((.....)))).))))(....))--))))-.)).((((((....-----...))-))))...... ( -29.40)
>consensus
GGCAGCUUGCUGAGUAUGCUCGUCAGCGAGCUGGCAAAGUUCCAGGAGAACAAGUAGGUGCUA__GCUG_ACCAUUGUUGUAUG_____CCUUU_AUUAAUUGUU
(.((((((((((((......).))))))))))).)...((((.....))))...................................................... (-17.43 = -18.10 +   0.67)

alignment

secondary structure

dotplot

Window 6

Location	4,399,643 – 4,399,749
Length	106
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	74.83
Mean single sequence MFE	-27.65
Consensus MFE	-22.16
Energy contribution	-22.22
Covariance contribution	0.06
Combinations/Pair	1.30
Mean z-score	-0.60
Structure conservation index	0.80
SVM decision value	0.12
SVM RNA-class probability	0.590940
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4399643 106 + 22407834
--UGCUUUGUUUA--UUUCAGGGUUAACGCGCGCUAUCAGCGUCGGGCGCGUCUUGACUUCGGUACCAAAUUGGGCAUGAAUUCGCCCUUCUAAGAAUCACGUCAAAGAC
--..(((((....--.(((.(((((((.(((((((..........))))))).)))))))............((((........))))......)))......))))).. ( -29.10)
>DroVir_CAF1 6415 95 + 1
--UU-----U-GCUUUUGCAGAGUAAAUGCGCGCUAUCAGCGUCGGGCGCGACUUGAUUUUGGCACCAAGCUGGGCAUGAAUUCGCCAUUCUAAAUGUAACCA-------
--..-----.-((((.((((((((.....((((((..........)))))).....))))).)))..))))..(((........)))................------- ( -22.70)
>DroEre_CAF1 5306 106 + 1
--UUCCUUGUUUA--UUUUAGGGUUAACGCGCGCUAUCAGCGUCGUGCGCGUCUUGACUUUGGUACCAAAUUGGGCAUGAAUUCGCCCUUCUAAGAAUCACGGCUAAGAC
--..(((((....--...))))).....((((((..........))))))((((((.((.((((........((((........))))........)))).)).)))))) ( -28.99)
>DroYak_CAF1 5307 106 + 1
--UUCCACGUUUA--UUUUAGGGUUAACGCGCGCUACCAGCGUCGAGCGCGUCUUGACUUUGGUACCAAGUUGGGCAUGAAUUCGCCCUUCUAAGAAUCACGGCUAUGAC
--.....(((...--((((((((((((.(((((((..........))))))).)))))((((....))))..((((........)))).)))))))...)))........ ( -29.60)
>DroMoj_CAF1 5601 93 + 1
---------U-UCCUUUGCAGAGUUAAUGCGCGCUAUCAGCGUCGAGCGCGUCUUGAUUUUGGCACCAAGCUGGGCAUGAAUUCGCCAUUUUAAAAGCUACCU-------
---------.-.....(((((((((((.(((((((..........))))))).)))))))).)))...((((.(((........)))........))))....------- ( -26.50)
>DroAna_CAF1 7901 99 + 1
UCUAUUCUAUCUA--UUUUAGGGUCAAUGCGCGCUAUCAGCGGCGGGCACGCCUUGAUUUUGGCACCAAACUGGGCAUGAACUCGCCCUUCUAAGAAU---------GAU
........(((..--(((((((((...(((.((((......)))).))).(((........)))))).....((((........))))..))))))..---------))) ( -29.00)
>consensus
__UUC__UGUUUA__UUUCAGGGUUAACGCGCGCUAUCAGCGUCGGGCGCGUCUUGACUUUGGCACCAAACUGGGCAUGAAUUCGCCCUUCUAAGAAUCACGG____GAC
..................(((((((((.(((((((..........))))))).)))))))))..........((((........))))...................... (-22.16 = -22.22 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:16 2006