Locus 3866

Sequence ID 2L_DroMel_CAF1
Location 11,319,702 – 11,319,829
Length 127
Max. P 0.809884
window6084 window6085 window6086

overview

Window 4

Location 11,319,702 – 11,319,799
Length 97
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.76
Mean single sequence MFE -33.02
Consensus MFE -23.51
Energy contribution -25.60
Covariance contribution 2.09
Combinations/Pair 1.15
Mean z-score -1.79
Structure conservation index 0.71
SVM decision value 0.64
SVM RNA-class probability 0.809884
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11319702 97 + 22407834
UGGCUCAGUGGUUGCGGCUGG-CGCAGUUUCA-----GCUUU--UUGCGCACCGCUGG--GGCACAGCGGUGAUUAAUUAAACCGACUGC---AACUCCAACUCAUGAUU
.......(..(((((((.(((-(((((.....-----.....--)))))((((((((.--....))))))))..........))).))))---)))..)........... ( -34.90)
>DroSec_CAF1 37094 97 + 1
UGGCUCAGUGGUUGCGGCUGG-CGCAGUUUUA-----GCUUU--UUGCGCAUCGCUGG--GGCACAGCGGUGAUUAAUUAAACCGACUGC---AGCUCCAACUCAUGAUU
....(((..(((((.((((..-.((((((...-----((...--..)).((((((((.--....))))))))............))))))---)))).)))))..))).. ( -33.80)
>DroEre_CAF1 39045 92 + 1
-----CAGUGGUUGCGGCUGG-CGAAGUUUUA-----GCUUU--UUGCGCACCGCUGG--GACACAGCGGUGAUUAAUUAAACCGAGCGC---AGCUCCAGCUCAUGAUU
-----..(((((((.((((((-(...((((..-----((...--..)).((((((((.--....)))))))).......))))...)).)---)))).)))).))).... ( -35.90)
>DroYak_CAF1 37464 93 + 1
-----CAGUGGUUGCGGCUGGUCGCAGUUUUA-----GCUUU--UUGCGCACCGCUGG--GGCACAGCGGUGAUUAAUUAAAUCGAGCGC---AGCUCCAACUCAUGAUU
-----..(((((((.(((((..(((.......-----((...--..)).((((((((.--....))))))))..............))))---)))).)))).))).... ( -35.00)
>DroAna_CAF1 33273 96 + 1
----UCAGUGUUUCUGUUCGCCGGCAGUUUGA-----GCUUUUUUUGUGCACCGCUGG--GGCACAGCGGUGAUUAAUUAAACCGACUGC---AGCUUCAACUCAUGAUU
----.(((.....)))...((..((((((.(.-----(.(((..(((..((((((((.--....))))))))..)))..)))))))))))---.)).............. ( -26.50)
>DroPer_CAF1 50513 96 + 1
-----CAUU------GGCAGU-UGCAGUUGCAUUGGUGCUUU--UUGUGCACCGCUGUGUGCCCCAGCGGUGAUUAAUUAAACCGACUGCCGUGGCUCCAACUCAUGAUU
-----..((------((.(((-..(....((((((((.....--(((..((((((((.......))))))))..)))....))))).))).)..)))))))......... ( -32.00)
>consensus
_____CAGUGGUUGCGGCUGG_CGCAGUUUUA_____GCUUU__UUGCGCACCGCUGG__GGCACAGCGGUGAUUAAUUAAACCGACUGC___AGCUCCAACUCAUGAUU
.....((..(((((.((((....((((((........((.......)).((((((((.......))))))))............))))))...)))).)))))..))... (-23.51 = -25.60 +   2.09)

alignment

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secondary structure

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Window 5

Location 11,319,702 – 11,319,799
Length 97
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.76
Mean single sequence MFE -29.38
Consensus MFE -16.80
Energy contribution -16.42
Covariance contribution -0.39
Combinations/Pair 1.22
Mean z-score -1.86
Structure conservation index 0.57
SVM decision value 0.05
SVM RNA-class probability 0.558981
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11319702 97 - 22407834
AAUCAUGAGUUGGAGUU---GCAGUCGGUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCGCAA--AAAGC-----UGAAACUGCG-CCAGCCGCAACCACUGAGCCA
..(((((.((((..(((---(((((((((((.......((((((((....--.)))))))).....--.))))-----)))..)))))-...))..)))))).))).... ( -31.22)
>DroSec_CAF1 37094 97 - 1
AAUCAUGAGUUGGAGCU---GCAGUCGGUUUAAUUAAUCACCGCUGUGCC--CCAGCGAUGCGCAA--AAAGC-----UAAAACUGCG-CCAGCCGCAACCACUGAGCCA
..(((((.(((((.((.---((((.((((..........)))))))))).--)))))..((((...--...((-----.......)).-.....))))..)).))).... ( -26.60)
>DroEre_CAF1 39045 92 - 1
AAUCAUGAGCUGGAGCU---GCGCUCGGUUUAAUUAAUCACCGCUGUGUC--CCAGCGGUGCGCAA--AAAGC-----UAAAACUUCG-CCAGCCGCAACCACUG-----
......(.(((((((((---((((..((((.....))))(((((((....--.)))))))))))..--..)))-----).........-))))))..........----- ( -28.50)
>DroYak_CAF1 37464 93 - 1
AAUCAUGAGUUGGAGCU---GCGCUCGAUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCGCAA--AAAGC-----UAAAACUGCGACCAGCCGCAACCACUG-----
.......((((..((((---((((..((((.....))))(((((((....--.)))))))))))..--..)))-----)..))))(((......)))........----- ( -31.00)
>DroAna_CAF1 33273 96 - 1
AAUCAUGAGUUGAAGCU---GCAGUCGGUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCACAAAAAAAGC-----UCAAACUGCCGGCGAACAGAAACACUGA----
..(((.....))).(((---(((((.(((((.......((((((((....--.))))))))........))))-----)...)))).))))...(((.....))).---- ( -27.56)
>DroPer_CAF1 50513 96 - 1
AAUCAUGAGUUGGAGCCACGGCAGUCGGUUUAAUUAAUCACCGCUGGGGCACACAGCGGUGCACAA--AAAGCACCAAUGCAACUGCA-ACUGCC------AAUG-----
........(((((.(((.((((.((.((((.....)))))).)))).)))...(((.(((((....--...)))))..(((....)))-.)))))------))).----- ( -31.40)
>consensus
AAUCAUGAGUUGGAGCU___GCAGUCGGUUUAAUUAAUCACCGCUGUGCC__CCAGCGGUGCGCAA__AAAGC_____UAAAACUGCG_CCAGCCGCAACCACUG_____
.....((((((((.((....))..))))))))......((((((((.......))))))))................................................. (-16.80 = -16.42 +  -0.39)

alignment

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secondary structure

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Window 6

Location 11,319,735 – 11,319,829
Length 94
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 85.22
Mean single sequence MFE -26.18
Consensus MFE -23.27
Energy contribution -22.80
Covariance contribution -0.47
Combinations/Pair 1.15
Mean z-score -1.65
Structure conservation index 0.89
SVM decision value 0.52
SVM RNA-class probability 0.768262
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11319735 94 - 22407834
---------AGU-CAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGGAGUU---GCAGUCGGUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCGCAA--AAA
---------...-...(((((((...(((((((.((.....)).)))))))....))---).))))............((((((((....--.)))))))).....--... ( -21.20)
>DroPse_CAF1 50131 100 - 1
---------AGUCCAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGGAGCCACGGCAGUCGGUUUAAUUAAUCACCGCUGGGGCACACAGCGGUGCACAA--AAA
---------.(((...(((((.....(((((((.((.....)).))))))).)))))..)))................((((((((.......)))))))).....--... ( -27.30)
>DroEre_CAF1 39073 91 - 1
-------------CAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGCUGGAGCU---GCGCUCGGUUUAAUUAAUCACCGCUGUGUC--CCAGCGGUGCGCAA--AAA
-------------...(((((.......(((((.((.....)).)))))...)))))---((((..((((.....))))(((((((....--.)))))))))))..--... ( -24.40)
>DroYak_CAF1 37493 103 - 1
CAGUAGUGGAGU-GAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGGAGCU---GCGCUCGAUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCGCAA--AAA
.....(((((((-(..(((((.....(((((((.((.....)).))))))).)))))---.)))))............((((((((....--.)))))))))))..--... ( -31.70)
>DroAna_CAF1 33303 102 - 1
CG---UUUGCGU-CAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGAAGCU---GCAGUCGGUUUAAUUAAUCACCGCUGUGCC--CCAGCGGUGCACAAAAAAA
((---.((((..-...(((((.....(((((((.((.....)).))))))).)))))---)))).))...........((((((((....--.)))))))).......... ( -25.20)
>DroPer_CAF1 50540 100 - 1
---------AGUCCAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGGAGCCACGGCAGUCGGUUUAAUUAAUCACCGCUGGGGCACACAGCGGUGCACAA--AAA
---------.(((...(((((.....(((((((.((.....)).))))))).)))))..)))................((((((((.......)))))))).....--... ( -27.30)
>consensus
_________AGU_CAAGGCUUAAAUAAAUUCGUCAUUAUAAAUCAUGAGUUGGAGCU___GCAGUCGGUUUAAUUAAUCACCGCUGUGCC__CCAGCGGUGCACAA__AAA
................(((((.....(((((((.((.....)).))))))).)))))...((....((((.....))))(((((((.......)))))))))......... (-23.27 = -22.80 +  -0.47)

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 11:03:18 2006