Locus 6617

Sequence ID 3L_DroMel_CAF1
Location 17,600,204 – 17,600,326
Length 122
Max. P 0.968703
window10767 window10768 window10769

overview

Window 7

Location 17,600,204 – 17,600,302
Length 98
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -27.32
Consensus MFE -21.25
Energy contribution -21.53
Covariance contribution 0.28
Combinations/Pair 1.09
Mean z-score -2.15
Structure conservation index 0.78
SVM decision value 1.63
SVM RNA-class probability 0.968703
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17600204 98 + 23771897
UUUCCCAACAUUUUUU-----UUUUGCUGAGACGACAGUGCGUAUGCGUA---------AUAUGCGUAAAUUGCUGUCGCCAGCAAUUUGAGCCGUCAAGGAAGCAUAAAUU
(((((...........-----..((((((.(.((((((((..(((((((.---------..)))))))...))))))))))))))).((((....)))))))))........ ( -29.00)
>DroSec_CAF1 12554 100 + 1
UUUUCCAACAUUUUUUUU-UUUUUUGCUGAGACGACAGUGCGUAUGCGUA---------AUAUGCGUAAAUUGCUGUCGCCAGCAAUUUAAGACGUCGAGGAAGCAUAAA--
.(((((............-....((((((.(.((((((((..(((((((.---------..)))))))...))))))))))))))).....(....)..)))))......-- ( -28.00)
>DroSim_CAF1 12622 101 + 1
UUUUCCAACAUUUUUUUUCUUUUUUGCUGAGACGACAGUGCGUAUGCGUA---------AUAUGCGUAAAUUGCUGUCGCCAGCAAUUUGAGCCGUCGCGGAAGCAUAAA--
..................(((..((((((.(.((((((((..(((((((.---------..)))))))...)))))))))))))))...))).....((....)).....-- ( -31.20)
>DroEre_CAF1 12205 94 + 1
UUUCGUAACUUU---------UUCUGCUGAGACGACAGUGCGUAUGCGUA---------AUAUGCGUAAUUUGCUGUCGCCAGCAAUUUGAGCCGUGGAGGAAACAUAAAUU
.((((...(((.---------...(((((.(.((((((((..(((((((.---------..)))))))...))))))))))))))....)))...))))(....)....... ( -27.80)
>DroYak_CAF1 12607 103 + 1
UUUUCGAACAUU---------UUGUGCUGAGACGACAGUGCGUAUGCGUAAUACGUGUAAUAUGCGUAAAUUGCUGUCGCCAGCAAUUUGAGCCGUCGAGGAAUCAUAAAUU
(((((((...((---------...(((((.(.((((((((..((((((((.((....)).))))))))...))))))))))))))....))....))))))).......... ( -33.70)
>DroAna_CAF1 14172 96 + 1
UUUUCUU-UACUCCUUAU-UUUUAUGCUGAGACAACAAGGCGUAUGCGUA---------AUAUCCGUAAAUUUCUAGUGACAGCAAUUUUAUUCCCUGAGA-----GAAAUU
.((((((-(.........-.....(((((.....((.(((.((.((((..---------.....)))).)).))).))..))))).............)))-----)))).. ( -14.23)
>consensus
UUUUCCAACAUUUUUU_____UUUUGCUGAGACGACAGUGCGUAUGCGUA_________AUAUGCGUAAAUUGCUGUCGCCAGCAAUUUGAGCCGUCGAGGAAGCAUAAAUU
........................(((((.(.((((((((..((((((((..........))))))))...))))))))))))))........................... (-21.25 = -21.53 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 17,600,204 – 17,600,302
Length 98
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -23.10
Consensus MFE -17.58
Energy contribution -18.30
Covariance contribution 0.72
Combinations/Pair 1.29
Mean z-score -1.96
Structure conservation index 0.76
SVM decision value 1.48
SVM RNA-class probability 0.957498
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17600204 98 - 23771897
AAUUUAUGCUUCCUUGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUCGUCUCAGCAAAA-----AAAAAAUGUUGGGAAA
.........((((..((((((..(((((((((....)))))))))........---------...((....))...)))))).(((((...-----......))))))))). ( -28.60)
>DroSec_CAF1 12554 100 - 1
--UUUAUGCUUCCUCGACGUCUUAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUCGUCUCAGCAAAAAA-AAAAAAAAUGUUGGAAAA
--....((((....((((((..((((((((((....)))))))))).))....---------...((....))...))))....)))).....-.................. ( -25.20)
>DroSim_CAF1 12622 101 - 1
--UUUAUGCUUCCGCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUCGUCUCAGCAAAAAAGAAAAAAAAUGUUGGAAAA
--....((((...(((((((...(((((((((....)))))))))........---------...((....)).)))))))...))))........................ ( -27.70)
>DroEre_CAF1 12205 94 - 1
AAUUUAUGUUUCCUCCACGGCUCAAAUUGCUGGCGACAGCAAAUUACGCAUAU---------UACGCAUACGCACUGUCGUCUCAGCAGAA---------AAAGUUACGAAA
..................((((....((((((((((((((.......))....---------...((....))..))))))..))))))..---------..))))...... ( -18.50)
>DroYak_CAF1 12607 103 - 1
AAUUUAUGAUUCCUCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAUUACACGUAUUACGCAUACGCACUGUCGUCUCAGCACAA---------AAUGUUCGAAAA
...............((((((..(((((((((....)))))))))............(((((.....)))))....))))))((((((...---------..)))).))... ( -24.60)
>DroAna_CAF1 14172 96 - 1
AAUUUC-----UCUCAGGGAAUAAAAUUGCUGUCACUAGAAAUUUACGGAUAU---------UACGCAUACGCCUUGUUGUCUCAGCAUAAAA-AUAAGGAGUA-AAGAAAA
((((((-----(..(((.((......)).))).....))))))).........---------......(((.(((((((.............)-)))))).)))-....... ( -14.02)
>consensus
AAUUUAUGCUUCCUCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU_________UACGCAUACGCACUGUCGUCUCAGCAAAA_____AAAAAAUGUUGGAAAA
......((((....((((((...(((((((((....)))))))))....................((....)).))))))....))))........................ (-17.58 = -18.30 +   0.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,600,232 – 17,600,326
Length 94
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 77.57
Mean single sequence MFE -24.67
Consensus MFE -16.04
Energy contribution -16.30
Covariance contribution 0.25
Combinations/Pair 1.22
Mean z-score -1.27
Structure conservation index 0.65
SVM decision value 0.14
SVM RNA-class probability 0.601645
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17600232 94 - 23771897
G---AUGCCUGAAGUGGAAUUCGCGUUAAUUUAUGCUUCCUUGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUC
.---.(((..(((......)))((((.....(((((..((.....))...(((((((((....)))))))))..))))).---------.))))....)))..... ( -26.00)
>DroSec_CAF1 12586 85 - 1
GG--AUGCCUGGAGUGGAA----------UUUAUGCUUCCUCGACGUCUUAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUC
((--(.((.((((......----------)))).)).)))..(((((..((((((((((....)))))))))).))....---------...((....))...))) ( -23.80)
>DroSim_CAF1 12655 85 - 1
GG--AUGCCUGGAGUGGAA----------UUUAUGCUUCCGCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU---------UACGCAUACGCACUGUC
..--(((((((..((((((----------.......))))))..)))...(((((((((....)))))))))..))))..---------...((....))...... ( -28.10)
>DroEre_CAF1 12229 94 - 1
G---AUGCCUGGCGUGGAAUUCGCAUUAAUUUAUGUUUCCUCCACGGCUCAAAUUGCUGGCGACAGCAAAUUACGCAUAU---------UACGCAUACGCACUGUC
.---((((..(.((((((....((((......))))....)))))).).....((((((....)))))).....))))..---------...((....))...... ( -27.60)
>DroYak_CAF1 12631 103 - 1
G---AUGCCUGGUGUGGAAUUCGCAUUAAUUUAUGAUUCCUCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAUUACACGUAUUACGCAUACGCACUGUC
(---(.(((...((.(((((...(((......)))))))).))..)))))(((((((((....)))))))))............(((((.....)))))....... ( -26.20)
>DroAna_CAF1 14203 92 - 1
GAACCUCCUUGGUGUGGAAUUUGCCUUAAUUUC-----UCUCAGGGAAUAAAAUUGCUGUCACUAGAAAUUUACGGAUAU---------UACGCAUACGCCUUGUU
.......(..((((((.(((...((..((((((-----(..(((.((......)).))).....)))))))...))..))---------).....))))))..).. ( -16.30)
>consensus
G___AUGCCUGGAGUGGAAUUCGC_UUAAUUUAUGCUUCCUCGACGGCUCAAAUUGCUGGCGACAGCAAUUUACGCAUAU_________UACGCAUACGCACUGUC
....(((((((..(.((((.................)))).)..)))...(((((((((....)))))))))..))))..............((....))...... (-16.04 = -16.30 +   0.25)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:47 2006