Locus 2248

Sequence ID 3R_DroMel_CAF1
Location 6,381,181 – 6,381,317
Length 136
Max. P 0.994191
window3643 window3644 window3645 window3646

overview

Window 3

Location 6,381,181 – 6,381,282
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 74.25
Mean single sequence MFE -25.72
Consensus MFE -16.53
Energy contribution -16.53
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.57
Structure conservation index 0.64
SVM decision value 2.46
SVM RNA-class probability 0.994191
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6381181 101 + 27905053
A-A--AGAAAUGAAAGGAACAAAAGUAUAAGUACGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUUAUAU
.-.--...................((((((((....(((((((((((-(((.....((((((....))))))))))))).....-.)))))))....)).)))))) ( -24.70)
>DroPse_CAF1 144034 87 + 1
-----GGCUGAGAAAC---CGAAA-U-------GGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUA-CGG
-----.(((.......---...((-(-------(((((.....((((-(((.....((((((....))))))))))))).....-))))))))...)))...-... ( -26.22)
>DroEre_CAF1 156398 101 + 1
A-U--AAGAAUGAAAGGAACGAGCGCAUAAGUGCGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUUAUAU
.-.--............((((.((((....))))..(((((((((((-(((.....((((((....))))))))))))).....-.))))))).....)))).... ( -29.10)
>DroWil_CAF1 241165 85 + 1
--------------AAAAAAAAA--AACCAA-ACAAAAUGGAACUUUUUCUGCCACGGCGCCAUUUGGCGCUACAA-AGAUAUUUUUUCCAUUGAAAGCAUA---A
--------------.........--......-....(((((((.....(((.....((((((....))))))....-)))......))))))).........---. ( -19.50)
>DroAna_CAF1 145482 100 + 1
UGUACGGACGCGAAAG---CGAAAACGCCAG-CCGAAAUGGAACUUU-UGCGCCAAGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCAUUAUAU
.....((.(((....)---))......)).(-(...(((((((((((-(((((((((......))))))))...))))).....-.)))))))....))....... ( -28.60)
>DroPer_CAF1 151235 87 + 1
-----GGCUGAGAAAC---CGAAA-U-------GGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUA-CGG
-----.(((.......---...((-(-------(((((.....((((-(((.....((((((....))))))))))))).....-))))))))...)))...-... ( -26.22)
>consensus
_____GGAAGAGAAAG___CGAAA_UA__AG__CGAAAUGGAACUUU_UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU_UUUCCAUUGAAAGCGUA_UAU
....................................(((((((.............((((((....))))))..............)))))))............. (-16.53 = -16.53 +  -0.00)

alignment

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secondary structure

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Window 4

Location 6,381,181 – 6,381,282
Length 101
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 74.25
Mean single sequence MFE -22.67
Consensus MFE -15.91
Energy contribution -15.91
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.70
SVM decision value 1.83
SVM RNA-class probability 0.978981
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6381181 101 - 27905053
AUAUAACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCGUACUUAUACUUUUGUUCCUUUCAUUUCU--U-U
.............(((((((.-.............(((((....)))))...((.(((-(((((................)))))))).)))))))))...--.-. ( -21.69)
>DroPse_CAF1 144034 87 - 1
CCG-UACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCC-------A-UUUCG---GUUUCUCAGCC-----
...-.........((((((((-.....(((((((...(((....)))((....)))))-)))).....)))))-------)-))..(---((......)))----- ( -22.90)
>DroEre_CAF1 156398 101 - 1
AUAUAACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCGCACUUAUGCGCUCGUUCCUUUCAUUCUU--A-U
....((((.....(((((((.-.....(((((((...(((....)))((....)))))-))))))))))).((((....))))..))))............--.-. ( -22.40)
>DroWil_CAF1 241165 85 - 1
U---UAUGCUUUCAAUGGAAAAAAUAUCU-UUGUAGCGCCAAAUGGCGCCGUGGCAGAAAAAGUUCCAUUUUGU-UUGGUU--UUUUUUUUU--------------
.---...(((..((((((((......(((-(..(.(((((....))))).)..).))).....))))))..)).-..))).--.........-------------- ( -19.60)
>DroAna_CAF1 145482 100 - 1
AUAUAAUGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCUUGGCGCA-AAAGUUCCAUUUCGG-CUGGCGUUUUCG---CUUUCGCGUCCGUACA
.......(((...(((((((.-.....(((((((...(((....)))((....)))))-)))))))))))..))-)..(((....((---(....)))..)))... ( -26.50)
>DroPer_CAF1 151235 87 - 1
CCG-UACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCC-------A-UUUCG---GUUUCUCAGCC-----
...-.........((((((((-.....(((((((...(((....)))((....)))))-)))).....)))))-------)-))..(---((......)))----- ( -22.90)
>consensus
AUA_AACGCUUUCAAUGGAAA_AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA_AAAGUUCCAUUUCG__CU__UA_UUUCG___CUUUCACAGCC_____
.............(((((((..........(((..(((((....)))))..))).........))))))).................................... (-15.91 = -15.91 +   0.00)

alignment

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secondary structure

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Window 5

Location 6,381,205 – 6,381,317
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.76
Mean single sequence MFE -28.12
Consensus MFE -14.77
Energy contribution -16.27
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.53
SVM decision value 0.86
SVM RNA-class probability 0.868443
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6381205 112 + 27905053
UAAGUACGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUUAUAUGGCCGGGC-GAAAAAGUUGUUUAAAUUUAGC--ACAAG--
(((((...((((..((((((-(.((((.((((..(((.(((((((.(((..((....-..))..)))..))))))).))))))))))-).)))))))))))..)))))..--.....-- ( -31.00)
>DroVir_CAF1 155592 101 + 1
CCAA-ACAAAAUGAAACUUU-U--GCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCAUUG------CGGGC---AAAAGUUGUUUAAAUUUAGC--AACCG--
....-.........((((((-(--(((.(((((((....)))))..(((..((....-..))..))).........------)))))---))))))).............--.....-- ( -26.70)
>DroWil_CAF1 241176 104 + 1
CCAA-ACAAAAUGGAACUUUUUCUGCCACGGCGCCAUUUGGCGCUACAA-AGAUAUUUUUUCCAUUGAAAGCAUA---AGGC--------AAAAGUUGUUUAAAUUUAGC--CCCACAG
..((-(((((((((((.....(((.....((((((....))))))....-)))......)))))))....((...---..))--------.....)))))).........--....... ( -24.00)
>DroMoj_CAF1 202325 103 + 1
CCAA-ACAAAAUGAAACUUU-U--GCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCAUUG------CAGGC---AAAAGUUGUUUAAAUUUAGCCAAACCA--
....-.........((((((-(--(((..((((((....)))))).(((..((....-..))..))).........------..)))---)))))))....................-- ( -26.60)
>DroAna_CAF1 145506 101 + 1
CCAG-CCGAAAUGGAACUUU-UGCGCCAAGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCAUUAUAUGGGC-----------GUUGUUUAAAUUUAGC--CCGGG--
((.(-(...(((((((((((-(((((((((......))))))))...))))).....-.)))))))....)).......((((-----------..............))--)))).-- ( -30.54)
>DroPer_CAF1 151252 106 + 1
------GGAAAUGGAACUUU-UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU-UUUCCAUUGAAAGCGUA-CGGGUACGGGCAGAAAAAGUUGUUUAAAUUUAGC--CCAAG--
------(((((.....((((-(((.....((((((....))))))))))))).....-))))).........(((-....)))((((.....(((((.....))))).))--))...-- ( -29.90)
>consensus
CCAA_ACAAAAUGGAACUUU_UGUGCCACGGCGCCAUUUGGCGCUACAAAAGAUAUU_UUUCCAUUGAAAGCAUU____GG_CGGGC___AAAAGUUGUUUAAAUUUAGC__ACCAG__
..............((((((....(((..((((((....)))))).(((..((.......))..))).................)))....))))))...................... (-14.77 = -16.27 +   1.50)

alignment

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secondary structure

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Window 6

Location 6,381,205 – 6,381,317
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.76
Mean single sequence MFE -28.43
Consensus MFE -15.16
Energy contribution -14.94
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -2.37
Structure conservation index 0.53
SVM decision value 1.00
SVM RNA-class probability 0.897239
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6381205 112 - 27905053
--CUUGU--GCUAAAUUUAAACAACUUUUUC-GCCCGGCCAUAUAACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCGUACUUA
--...((--((.((((......(((((((..-(((((((........(((..(((.(((..-....))).))).)))(((....))))))).)))..)-))))))..)))).))))... ( -31.40)
>DroVir_CAF1 155592 101 - 1
--CGGUU--GCUAAAUUUAAACAACUUUU---GCCCG------CAAUGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGC--A-AAAGUUUCAUUUUGU-UUGG
--.....--.((((((..((..(((((((---(((((------(...(((..(((.(((..-....))).))).)))(((....)))).)).)))--)-))))))...))..))-)))) ( -29.00)
>DroWil_CAF1 241176 104 - 1
CUGUGGG--GCUAAAUUUAAACAACUUUU--------GCCU---UAUGCUUUCAAUGGAAAAAAUAUCU-UUGUAGCGCCAAAUGGCGCCGUGGCAGAAAAAGUUCCAUUUUGU-UUGG
..(((((--((..................--------))))---)))......(((((((......(((-(..(.(((((....))))).)..).))).....)))))))....-.... ( -26.27)
>DroMoj_CAF1 202325 103 - 1
--UGGUUUGGCUAAAUUUAAACAACUUUU---GCCUG------CAAUGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGC--A-AAAGUUUCAUUUUGU-UUGG
--........((((((..((..(((((((---(((.(------(...(((..(((.(((..-....))).))).)))(((....)))))...)))--)-))))))...))..))-)))) ( -28.90)
>DroAna_CAF1 145506 101 - 1
--CCCGG--GCUAAAUUUAAACAAC-----------GCCCAUAUAAUGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCUUGGCGCA-AAAGUUCCAUUUCGG-CUGG
--.((((--((..............-----------)))).......(((...(((((((.-.....(((((((...(((....)))((....)))))-)))))))))))..))-).)) ( -28.94)
>DroPer_CAF1 151252 106 - 1
--CUUGG--GCUAAAUUUAAACAACUUUUUCUGCCCGUACCCG-UACGCUUUCAAUGGAAA-AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA-AAAGUUCCAUUUCC------
--...((--((.....................))))(((....-)))......(((((((.-.....(((((((...(((....)))((....)))))-)))))))))))...------ ( -26.10)
>consensus
__CUGGG__GCUAAAUUUAAACAACUUUU___GCCCG_CC____AAUGCUUUCAAUGGAAA_AAUAUCUUUUGUAGCGCCAAAUGGCGCCGUGGCACA_AAAGUUCCAUUUCGU_UUGG
.....................................................(((((((..........(((..(((((....)))))..))).........)))))))......... (-15.16 = -14.94 +  -0.22)

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 10:30:49 2006