Locus 6896

Sequence ID 3L_DroMel_CAF1
Location 18,600,083 – 18,600,218
Length 135
Max. P 0.972880
window11177 window11178 window11179

overview

Window 7

Location 18,600,083 – 18,600,189
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.12
Mean single sequence MFE -29.42
Consensus MFE -19.26
Energy contribution -19.35
Covariance contribution 0.09
Combinations/Pair 1.08
Mean z-score -2.95
Structure conservation index 0.65
SVM decision value 1.24
SVM RNA-class probability 0.935079
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18600083 106 + 23771897
AUGAGAUAC-CACUAAUUGGCCAUAAAAUUGUAUGAAAUUCAUGUGCCGGU------UUUUCC----CACUUUCGUGGCCAAUUAGUCACCU-AAAAUGUGGUUUUUGGUCAAUUUUU--
..(((((((-(((((((((((((..(((.((((((.....))))....((.------....))----)).)))..)))))))))))).(((.-.......)))....)))..))))).-- ( -27.20)
>DroSec_CAF1 11748 95 + 1
AUGAGAUAC-CACUAAUUGGCCAUAAAAUUGUAUGAAAUUCAUGUGCCGGU------U-UUCC----CACUUUCGUGGCCAAUUAGUCACCU-AAAAUGUG-U--UCGGU-------U--
.......((-(((((((((((((..(((.((((((.....))))....((.------.-..))----)).)))..))))))))))))(((..-.....)))-.--..)))-------.-- ( -25.10)
>DroSim_CAF1 11555 97 + 1
AUGAGAUAC-CACUAAUUGGCCAUAAAAUUGCAUGAAAUUCAUGUGCUGGU------UUUUCC----CACUUUCGUGGCCAAUUAGUCACCU-AAAAUGUGGU--UCGGU-------C--
.......((-(((((((((((((..(((..(((((.....)))))..(((.------.....)----)).)))..)))))))))))).(((.-.......)))--..)))-------.-- ( -30.40)
>DroYak_CAF1 12649 104 + 1
AUGAGAUAC-CACUAAUUGGCCAUAAAGCUGUAUGAAAUUCAUGUGCAGGU------UAUUCC----CACUUUUGUGGCCAAUUAGUCACCU-AAAAUGUGGC--UCGGUCAAUUUUA--
.((((((((-(..((((((((((((((((...(((.....)))..)).((.------.....)----)...))))))))))))))(((((..-.....)))))--..)))..))))))-- ( -31.20)
>DroAna_CAF1 10530 102 + 1
AUGAGAUAC-CACUAAUUGGCCAUAAAAUUAUAUGAAUUUCAUGUGGCGGU------UUUU-C----CACUUUCGUGGCCAGUUAGUCACCC-AAAAUGUGGU--UU-UUCAAUAAUU--
.(((((.((-(((((((((((((..((((((((((.....))))))).((.------....-)----)..)))..)))))))))))).((..-.....)))))--.)-))))......-- ( -30.90)
>DroPer_CAF1 13862 119 + 1
AUGGGAUGCCCACUAAUUGGCCAUAAAAUGUUAUAAAUUUCAUGCGUCGGUUUGGGUUUUUCCCCAUCGCUUACGUUGCCAAUUAGUCACCUCAAAAUGUGGCA-UGGGUCAAUAUUUGG
.......(((((.(((((((((((.((((.......)))).)))(((.(((.((((......))))..))).)))..))))))))(((((........))))).-))))).......... ( -31.70)
>consensus
AUGAGAUAC_CACUAAUUGGCCAUAAAAUUGUAUGAAAUUCAUGUGCCGGU______UUUUCC____CACUUUCGUGGCCAAUUAGUCACCU_AAAAUGUGGU__UCGGUCAAU_UUU__
...........(((((((((((((........(((.....)))(((..((...........))....)))....)))))))))))))(((........)))................... (-19.26 = -19.35 +   0.09)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,600,083 – 18,600,189
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.12
Mean single sequence MFE -31.40
Consensus MFE -20.10
Energy contribution -20.38
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -4.00
Structure conservation index 0.64
SVM decision value 1.70
SVM RNA-class probability 0.972880
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18600083 106 - 23771897
--AAAAAUUGACCAAAAACCACAUUUU-AGGUGACUAAUUGGCCACGAAAGUG----GGAAAA------ACCGGCACAUGAAUUUCAUACAAUUUUAUGGCCAAUUAGUG-GUAUCUCAU
--........(((....(((.......-.))).((((((((((((..(((((.----((....------.)).))..(((.....)))....)))..)))))))))))))-))....... ( -30.90)
>DroSec_CAF1 11748 95 - 1
--A-------ACCGA--A-CACAUUUU-AGGUGACUAAUUGGCCACGAAAGUG----GGAA-A------ACCGGCACAUGAAUUUCAUACAAUUUUAUGGCCAAUUAGUG-GUAUCUCAU
--.-------(((..--.-(((.....-..)))((((((((((((..(((((.----((..-.------.)).))..(((.....)))....)))..)))))))))))))-))....... ( -30.30)
>DroSim_CAF1 11555 97 - 1
--G-------ACCGA--ACCACAUUUU-AGGUGACUAAUUGGCCACGAAAGUG----GGAAAA------ACCAGCACAUGAAUUUCAUGCAAUUUUAUGGCCAAUUAGUG-GUAUCUCAU
--.-------(((..--(((.......-.))).((((((((((((..(((.((----(.....------.)))...((((.....))))...)))..)))))))))))))-))....... ( -32.10)
>DroYak_CAF1 12649 104 - 1
--UAAAAUUGACCGA--GCCACAUUUU-AGGUGACUAAUUGGCCACAAAAGUG----GGAAUA------ACCUGCACAUGAAUUUCAUACAGCUUUAUGGCCAAUUAGUG-GUAUCUCAU
--........(((..--(((.......-.))).((((((((((((.(((.(..----((....------.))..)..(((.....))).....))).)))))))))))))-))....... ( -29.90)
>DroAna_CAF1 10530 102 - 1
--AAUUAUUGAA-AA--ACCACAUUUU-GGGUGACUAACUGGCCACGAAAGUG----G-AAAA------ACCGCCACAUGAAAUUCAUAUAAUUUUAUGGCCAAUUAGUG-GUAUCUCAU
--......(((.-(.--(((((...((-((....)))).((((((..((((((----(-....------....))))(((.....)))....)))..))))))....)))-)).).))). ( -30.60)
>DroPer_CAF1 13862 119 - 1
CCAAAUAUUGACCCA-UGCCACAUUUUGAGGUGACUAAUUGGCAACGUAAGCGAUGGGGAAAAACCCAAACCGACGCAUGAAAUUUAUAACAUUUUAUGGCCAAUUAGUGGGCAUCCCAU
........((.(((.-.(((.(.....).))).((((((((((..(((......((((......)))).....)))((((((((.......)))))))))))))))))))))))...... ( -34.60)
>consensus
__AAA_AUUGACCGA__ACCACAUUUU_AGGUGACUAAUUGGCCACGAAAGUG____GGAAAA______ACCGGCACAUGAAUUUCAUACAAUUUUAUGGCCAAUUAGUG_GUAUCUCAU
...................(((........)))((((((((((((.(((((((....((...........))..)))(((.....)))....)))).))))))))))))........... (-20.10 = -20.38 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,600,122 – 18,600,218
Length 96
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 79.90
Mean single sequence MFE -23.87
Consensus MFE -15.62
Energy contribution -15.82
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.65
SVM decision value 0.50
SVM RNA-class probability 0.761938
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18600122 96 - 23771897
UUUUUCUCUGC---------UGGAUUAUAGGGUAUCACAAAAAUUGACCAAAAACCACAUUUUAGGUGACUAAUUGGCCACGAAAGUGGGAAAAACCGGCACAUG
........(((---------(((.......(((.............))).....(((....((((....)))).)))((((....))))......)))))).... ( -25.12)
>DroSec_CAF1 11787 85 - 1
UUUUUCUCUGC---------UGGAUUACAGGGUAUCACA-------ACCGA--A-CACAUUUUAGGUGACUAAUUGGCCACGAAAGUGGGAA-AACCGGCACAUG
........(((---------(((.......(((......-------)))..--.-..((..((((....)))).)).((((....))))...-..)))))).... ( -25.30)
>DroSim_CAF1 11594 87 - 1
UUUUCCUCUGC---------UGGAUUACAGGGUAUCACG-------ACCGA--ACCACAUUUUAGGUGACUAAUUGGCCACGAAAGUGGGAAAAACCAGCACAUG
........(((---------(((.......(((......-------)))..--.(((....((((....)))).)))((((....))))......)))))).... ( -27.20)
>DroEre_CAF1 12517 94 - 1
CUUUCCUCUGC---------UGGAUUAUAGGGUAUCACAAAAAUUGACCAA--ACCUCAUGUUAGGUGACUAAUUGGCCACGAAAGUGGGAAAAACCGGCACAUG
........(((---------(((.......(((.............)))..--.((....(((((....))))).))((((....))))......)))))).... ( -25.82)
>DroYak_CAF1 12688 94 - 1
CUUUCCUCUGC---------CGGAUUAUAGGGUAUCACUAAAAUUGACCGA--GCCACAUUUUAGGUGACUAAUUGGCCACAAAAGUGGGAAUAACCUGCACAUG
...(((.....---------.)))...((((.(((..(((...(((...(.--((((....((((....)))).))))).)))...)))..))).))))...... ( -19.80)
>DroAna_CAF1 10569 99 - 1
--AUCCCCCGCACACUUCAAUCGACUGAAAGGUAUGAAAAUUAUUGAA-AA--ACCACAUUUUGGGUGACUAACUGGCCACGAAAGUGG-AAAAACCGCCACAUG
--.......((....((((......)))).(((...............-..--.(((....((((....)))).)))((((....))))-....)))))...... ( -20.00)
>consensus
UUUUCCUCUGC_________UGGAUUAUAGGGUAUCACAAAAAUUGACCAA__ACCACAUUUUAGGUGACUAAUUGGCCACGAAAGUGGGAAAAACCGGCACAUG
..............................(((.....................(((....((((....)))).)))((((....)))).....)))........ (-15.62 = -15.82 +   0.19)

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 12:32:25 2006