Locus 5033

Sequence ID 2L_DroMel_CAF1
Location 14,431,488 – 14,431,677
Length 189
Max. P 0.903598
window7998 window7999 window8000 window8001 window8002

overview

Window 8

Location 14,431,488 – 14,431,584
Length 96
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 77.74
Mean single sequence MFE -34.17
Consensus MFE -16.82
Energy contribution -17.57
Covariance contribution 0.75
Combinations/Pair 1.12
Mean z-score -2.38
Structure conservation index 0.49
SVM decision value 1.03
SVM RNA-class probability 0.903598
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14431488 96 + 22407834
CACCUAAAU-----------------GGGGGCGCUAAUCUCUGCAAC--AGAGAUUAACAGCCGA--GCAGACACAGAAACCAAUUUUGUGUGCCGGCCAACUGCCGGCCAGGCAGG
..(((....-----------------)))(((..(((((((((...)--))))))))...)))..--((..((((((((.....))))))))((((((.....))))))...))... ( -38.20)
>DroPse_CAF1 30487 107 + 1
CAUCCAAAUAGAGGCGGGAGCGGGUUGGGGGCGCUAAUCUCUGCAAC--ACAGAUUAACUGCCGA--ACAGACACAGAAACCAAUUUUGUGUGCCAGUCAG------CCCAGGCAGC
...((........((....))(((((((.(((..((((((.((...)--).)))))).(((....--.)))((((((((.....)))))))))))..))))------))).)).... ( -32.30)
>DroSec_CAF1 21771 93 + 1
CACCUAAAU-----------------GGGGGCGCUAAUCUCUGCAAC--AGAGAUUAACAGCCGA--GCAGACACAGAAACCAAUUUUGUGUGCCGGCCAACU---GGCCAGGCAGG
..(((....-----------------)))(((..(((((((((...)--))))))))...)))..--....((((((((.....))))))))(((((((....---)))).)))... ( -37.20)
>DroEre_CAF1 23141 95 + 1
CACCUAAAU-----------------GGGGGCGCUAAUCUCUGCAAC--AGAGAUUAACAACCGGGCGCAGACACAGAAACCAAUUUUCUGUGCCAGCCAACU---GGCCAGGCAGG
..(((...(-----------------((((..(.(((((((((...)--)))))))).)..)).(((...(.((((((((.....)))))))))..)))....---..)))...))) ( -32.50)
>DroAna_CAF1 14215 94 + 1
CGCCUAAAU-----------------GGGGGCGCUAAUCUCUGCAACACAGAGAUUAACAAACGAGAACAGACUCGGCAACCAAUUUUGGGUUCCAGCC---U---GGCCAGCCUGC
.((((((((-----------------((..(((.(((((((((.....))))))))).)...((((......))))))..)))..)))))))....((.---.---((....)).)) ( -31.90)
>DroPer_CAF1 17171 107 + 1
CAUCCAAAUAGAGGCGGGAGCGGGUUGGGGGCGCUAAUCUCUGCAAC--ACAGAUUAACAGCCGA--ACAGACACAGAAACCAAUUUUGUGUGCCAGUCAG------CCCAGGCAGC
...((........((....))(((((((.((((((....((((....--.)))).....)))...--....((((((((.....)))))))))))..))))------))).)).... ( -32.90)
>consensus
CACCUAAAU_________________GGGGGCGCUAAUCUCUGCAAC__AGAGAUUAACAGCCGA__ACAGACACAGAAACCAAUUUUGUGUGCCAGCCAA_U___GGCCAGGCAGC
...........................(((((..((((((((.......))))))))...)))........((((((((.....)))))))).)).(((............)))... (-16.82 = -17.57 +   0.75)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,431,488 – 14,431,584
Length 96
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.74
Mean single sequence MFE -35.37
Consensus MFE -19.60
Energy contribution -20.55
Covariance contribution 0.95
Combinations/Pair 1.12
Mean z-score -1.88
Structure conservation index 0.55
SVM decision value 0.52
SVM RNA-class probability 0.768099
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14431488 96 - 22407834
CCUGCCUGGCCGGCAGUUGGCCGGCACACAAAAUUGGUUUCUGUGUCUGC--UCGGCUGUUAAUCUCU--GUUGCAGAGAUUAGCGCCCCC-----------------AUUUAGGUG
((((..(((..((((((((((.((((((.(((.....))).)))))).))--.)))))((((((((((--(...)))))))))))))).))-----------------)..)))).. ( -40.00)
>DroPse_CAF1 30487 107 - 1
GCUGCCUGGG------CUGACUGGCACACAAAAUUGGUUUCUGUGUCUGU--UCGGCAGUUAAUCUGU--GUUGCAGAGAUUAGCGCCCCCAACCCGCUCCCGCCUCUAUUUGGAUG
((.(..((((------..(((.((((((.(((.....))).)))))).))--).(((.((((((((.(--(...)).)))))))))))))))..).)).....((.......))... ( -30.20)
>DroSec_CAF1 21771 93 - 1
CCUGCCUGGCC---AGUUGGCCGGCACACAAAAUUGGUUUCUGUGUCUGC--UCGGCUGUUAAUCUCU--GUUGCAGAGAUUAGCGCCCCC-----------------AUUUAGGUG
...((((((((---....))))((((((.(((.....))).))))))...--..(((.((((((((((--(...))))))))))))))...-----------------....)))). ( -36.50)
>DroEre_CAF1 23141 95 - 1
CCUGCCUGGCC---AGUUGGCUGGCACAGAAAAUUGGUUUCUGUGUCUGCGCCCGGUUGUUAAUCUCU--GUUGCAGAGAUUAGCGCCCCC-----------------AUUUAGGUG
((((..(((..---....(((.((((((((((.....))))))))))...))).((.(((((((((((--(...)))))))))))).))))-----------------)..)))).. ( -39.70)
>DroAna_CAF1 14215 94 - 1
GCAGGCUGGCC---A---GGCUGGAACCCAAAAUUGGUUGCCGAGUCUGUUCUCGUUUGUUAAUCUCUGUGUUGCAGAGAUUAGCGCCCCC-----------------AUUUAGGCG
..((((.(..(---(---((((((((((.......)))).)).))))))..)..))))(((((((((((.....)))))))))))(((...-----------------.....))). ( -35.60)
>DroPer_CAF1 17171 107 - 1
GCUGCCUGGG------CUGACUGGCACACAAAAUUGGUUUCUGUGUCUGU--UCGGCUGUUAAUCUGU--GUUGCAGAGAUUAGCGCCCCCAACCCGCUCCCGCCUCUAUUUGGAUG
((.(..((((------..(((.((((((.(((.....))).)))))).))--).(((.((((((((.(--(...)).)))))))))))))))..).)).....((.......))... ( -30.20)
>consensus
CCUGCCUGGCC___A_UUGGCUGGCACACAAAAUUGGUUUCUGUGUCUGC__UCGGCUGUUAAUCUCU__GUUGCAGAGAUUAGCGCCCCC_________________AUUUAGGUG
...(((.((((.......))))((((((.(((.....))).)))))).......))).((((((((((.......))))))))))................................ (-19.60 = -20.55 +   0.95)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,431,544 – 14,431,660
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.10
Mean single sequence MFE -39.73
Consensus MFE -23.44
Energy contribution -23.64
Covariance contribution 0.20
Combinations/Pair 1.17
Mean z-score -2.68
Structure conservation index 0.59
SVM decision value 0.57
SVM RNA-class probability 0.785362
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14431544 116 + 22407834
AAACCAAUUUUGUGUGCCGGCCAACUGCCGGCCAGGCAGGAAG--GCAGAAUG-GCUCUUGGUCGAGUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCUUUCUGGGUAAUUUGACACUU
..(((((((((((.(((((((.....))))).)).)))))).(--((......-))).))))).(((((.(((.(.((((((((((...-......)))))))))).)...))).))))) ( -44.20)
>DroPse_CAF1 30560 114 + 1
AAACCAAUUUUGUGUGCCAGUCAG------CCCAGGCAGCAGGCAACAGAAUGGGCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAAAAUUUACGGCUUUCUGGGUAAUUUGACACUU
...(((.((((((.((((.((..(------(....)).)).))))))))))))).......(((((((.((.....((((((((((..........)))))))))))).))))))).... ( -39.60)
>DroGri_CAF1 44659 103 + 1
CAACCAAUUUUGUGUGACCGG----------UCGGU---GACU--GGUGAACG-GUGCUCGGCCAAAUGACAGCAGCCAGAAGGCCCGA-AUUUACGGCUUUCUGGGUAAUUUGACACUC
...........((((.(..((----------(((((---.(((--(.....))-)))).)))))............((((((((((...-......))))))))))......).)))).. ( -33.30)
>DroEre_CAF1 23199 113 + 1
AAACCAAUUUUCUGUGCCAGCCAACU---GGCCAGGCAGGAAG--GCAGAAUG-GCUCUUGGUCGAGUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCCUUCUGGGUAAUUUGACACUU
..(((((.((((((((((((....))---)))...)))))))(--((......-))).))))).(((((.(((.(.((((((((((...-......)))))))))).)...))).))))) ( -43.20)
>DroAna_CAF1 14275 110 + 1
CAACCAAUUUUGGGUUCCAGCC---U---GGCCAGCCUGCCUA--GCAGAAUG-GCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCUUUCUGGGUAAUUUGACACUU
....(((....((((....)))---)---(((((..((((...--))))..))-))).)))(((((((.((.....((((((((((...-......)))))))))))).))))))).... ( -38.50)
>DroPer_CAF1 17244 114 + 1
AAACCAAUUUUGUGUGCCAGUCAG------CCCAGGCAGCAGGCAACAGAAUGGGCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAAAAUUUACGGCUUUCUGGGUAAUUUGACACUU
...(((.((((((.((((.((..(------(....)).)).))))))))))))).......(((((((.((.....((((((((((..........)))))))))))).))))))).... ( -39.60)
>consensus
AAACCAAUUUUGUGUGCCAGCCA_______GCCAGGCAGCAAG__GCAGAAUG_GCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAA_AUUUACGGCUUUCUGGGUAAUUUGACACUU
..............((((................)))).......................(((((((.((.....((((((((((..........)))))))))))).))))))).... (-23.44 = -23.64 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,431,544 – 14,431,660
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.10
Mean single sequence MFE -35.98
Consensus MFE -21.30
Energy contribution -21.36
Covariance contribution 0.06
Combinations/Pair 1.20
Mean z-score -1.95
Structure conservation index 0.59
SVM decision value -0.02
SVM RNA-class probability 0.522775
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14431544 116 - 22407834
AAGUGUCAAAUUACCCAGAAAGCCGUAAAU-UUAGGCCUUCUGGCUGCUGUCACUCGACCAAGAGC-CAUUCUGC--CUUCCUGCCUGGCCGGCAGUUGGCCGGCACACAAAAUUGGUUU
..(((((.......((((((.(((......-...))).))))))((...(((....)))..)).((-((..((((--(..((.....))..))))).)))).)))))............. ( -39.30)
>DroPse_CAF1 30560 114 - 1
AAGUGUCAAAUUACCCAGAAAGCCGUAAAUUUUAGGCCUUCUGGCUGCUGUCAUUUGACCAAGAGCCCAUUCUGUUGCCUGCUGCCUGGG------CUGACUGGCACACAAAAUUGGUUU
..(.(((((((.((((((((.(((..........))).)))))).....)).))))))))..(((((.(((.(((((((..(.((....)------).)...)))).))).))).))))) ( -36.30)
>DroGri_CAF1 44659 103 - 1
GAGUGUCAAAUUACCCAGAAAGCCGUAAAU-UCGGGCCUUCUGGCUGCUGUCAUUUGGCCGAGCAC-CGUUCACC--AGUC---ACCGA----------CCGGUCACACAAAAUUGGUUG
..(.(((((((.((((((((.(((......-...))).)))))).....)).))))))))((((..-.))))...--....---..(((----------(((((........)))))))) ( -26.70)
>DroEre_CAF1 23199 113 - 1
AAGUGUCAAAUUACCCAGAAGGCCGUAAAU-UUAGGCCUUCUGGCUGCUGUCACUCGACCAAGAGC-CAUUCUGC--CUUCCUGCCUGGCC---AGUUGGCUGGCACAGAAAAUUGGUUU
.((((.((...((.((((((((((......-...)))))))))).)).)).)))).......((((-(((((((.--.....((((.((((---....)))))))))))))...)))))) ( -43.00)
>DroAna_CAF1 14275 110 - 1
AAGUGUCAAAUUACCCAGAAAGCCGUAAAU-UUAGGCCUUCUGGCUGCUGUCAUUUGACCAAGAGC-CAUUCUGC--UAGGCAGGCUGGCC---A---GGCUGGAACCCAAAAUUGGUUG
(((((.((...((.((((((.(((......-...))).)))))).)).)).)))))(((((((.((-((..((((--...))))..)))))---.---...(((...)))...)))))). ( -34.30)
>DroPer_CAF1 17244 114 - 1
AAGUGUCAAAUUACCCAGAAAGCCGUAAAUUUUAGGCCUUCUGGCUGCUGUCAUUUGACCAAGAGCCCAUUCUGUUGCCUGCUGCCUGGG------CUGACUGGCACACAAAAUUGGUUU
..(.(((((((.((((((((.(((..........))).)))))).....)).))))))))..(((((.(((.(((((((..(.((....)------).)...)))).))).))).))))) ( -36.30)
>consensus
AAGUGUCAAAUUACCCAGAAAGCCGUAAAU_UUAGGCCUUCUGGCUGCUGUCAUUUGACCAAGAGC_CAUUCUGC__CCUCCUGCCUGGC_______UGGCUGGCACACAAAAUUGGUUU
(((((.((...((.((((((.(((..........))).)))))).)).)).)))))(((((((((....)))...........(((................)))........)))))). (-21.30 = -21.36 +   0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,431,584 – 14,431,677
Length 93
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -27.17
Consensus MFE -22.82
Energy contribution -22.40
Covariance contribution -0.42
Combinations/Pair 1.16
Mean z-score -1.44
Structure conservation index 0.84
SVM decision value -0.00
SVM RNA-class probability 0.531088
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14431584 93 + 22407834
AAG--GCAGAAUG-GCUCUUGGUCGAGUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCUUUCUGGGUAAUUUGACACUU-CGGACAG---AAUAAA-C-GAG
..(--((......-))).(((..((((((.(((.(.((((((((((...-......)))))))))).)...))).))).)-))..)))---......-.-... ( -27.40)
>DroPse_CAF1 30594 98 + 1
AGGCAACAGAAUGGGCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAAAAUUUACGGCUUUCUGGGUAAUUUGACACUUUUCGACAG---AAUAUA-C-GAG
.(....)..........(((((((((((.((.....((((((((((..........)))))))))))).)))))))....(((....)---))....-)-))) ( -26.40)
>DroGri_CAF1 44686 95 + 1
ACU--GGUGAACG-GUGCUCGGCCAAAUGACAGCAGCCAGAAGGCCCGA-AUUUACGGCUUUCUGGGUAAUUUGACACUC-UGGACAGCAGCACAAUCCC---
...--((.((...-((((((..(((..((.(((.(.((((((((((...-......)))))))))).)...))).))...-)))...).)))))..))))--- ( -28.90)
>DroEre_CAF1 23236 93 + 1
AAG--GCAGAAUG-GCUCUUGGUCGAGUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCCUUCUGGGUAAUUUGACACUU-UGGACAG---AAUGAA-C-GAG
(((--((......-)).))).((((((((.(((.(.((((((((((...-......)))))))))).)...))).)))))-..)))..---......-.-... ( -29.50)
>DroAna_CAF1 14309 93 + 1
CUA--GCAGAAUG-GCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAA-AUUUACGGCUUUCUGGGUAAUUUGACACUU-UGGACAG---AAUAAU-C-GAG
..(--((......-)))(((((((((((.((.....((((((((((...-......)))))))))))).))))))).((.-.....))---......-)-))) ( -24.40)
>DroPer_CAF1 17278 98 + 1
AGGCAACAGAAUGGGCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAAAAUUUACGGCUUUCUGGGUAAUUUGACACUUUUCGACAG---AAUAUA-C-GAG
.(....)..........(((((((((((.((.....((((((((((..........)))))))))))).)))))))....(((....)---))....-)-))) ( -26.40)
>consensus
AAG__GCAGAAUG_GCUCUUGGUCAAAUGACAGCAGCCAGAAGGCCUAA_AUUUACGGCUUUCUGGGUAAUUUGACACUU_UGGACAG___AAUAAA_C_GAG
.....................(((((((.((.....((((((((((..........)))))))))))).)))))))........................... (-22.82 = -22.40 +  -0.42)

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 11:34:09 2006