Locus 3771

Sequence ID 3R_DroMel_CAF1
Location 10,233,599 – 10,233,733
Length 134
Max. P 0.875106
window6038 window6039 window6040

overview

Window 8

Location 10,233,599 – 10,233,714
Length 115
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.44
Mean single sequence MFE -26.10
Consensus MFE -14.29
Energy contribution -15.32
Covariance contribution 1.03
Combinations/Pair 1.13
Mean z-score -2.15
Structure conservation index 0.55
SVM decision value 0.82
SVM RNA-class probability 0.858924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10233599 115 + 27905053
-CAGGCUC-ACAAAUAAUUAUAGAAAUUAUGAAUCAA-GCCCCAUCGGACAGACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGACCGCUAAUUCGCUGGCAGGACCACCGGCGCA
-..((((.-....((((((.....))))))......)-)))...((((.....(((((((((....((.....))..))))))))).((((((......)))).))....)))).... ( -25.90)
>DroVir_CAF1 108889 109 + 1
-AAAUAUCUGACCAUAAUUAUAGAAAUUAUGAAACGC-AGCC-------UUCACUGUUAUUAUAAACCACUCACGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCA
-...........(((((((.....)))))))...(((-.(((-------....(((((((((...............)))))))))((((.....)))).))).((....)).))).. ( -25.36)
>DroGri_CAF1 96540 110 + 1
AAAAAUUCUAGUCAUAAUUAUAGAAAUUAUGAAAUAC-AGUC-------UGCACUGUUAUUAUAAACCACUCACGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCA
...........((((((((.....))))))))....(-(((.-------.((.(((((((((...............)))))))))...))..))))(((((........)))))... ( -26.36)
>DroWil_CAF1 105601 112 + 1
-CGGUCUAUGCUAAUAAUUAUAGAAAUUAUGAAACUCAGCCAC-----ACACACUAUUAUUAUAAACCACUCAGGCUUAAUAACAGGUCGCUAAUUGGCUGGCAGGACCACCAGCACA
-.(((((.(((..((((((.....))))))......((((((.-----.....((.((((((....((.....))..)))))).)).........))))))))))))))......... ( -24.06)
>DroAna_CAF1 83407 111 + 1
-CAGGUCC-GAGCCUAAUUAUUGAAAUAAUGAAUCAU-GCCCCA----GUACGCUGUUAUUAUAAACCACUCAGGCUUAAUAACAGGCCGCUAAUUGGUCGGCAGGACCACCGGCGAA
-..(((((-((.....(((((....)))))...)).(-((((((----((.(((((((((((....((.....))..)))))))))..))...)))))..)))))))))......... ( -29.70)
>DroPer_CAF1 102858 111 + 1
-CAGACUC-UGUCAUAAUUAUAGAAAUUAUGAGUCAU-GCUUGA----CCACACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGUCCACUAAUUGGCUGGCAGGACCACCAAGACC
-.....((-(.((((((((.....))))))))(((.(-(((.(.----(((.((((((((((....((.....))..))))))))))........)))).)))).))).....))).. ( -25.20)
>consensus
_CAGACUC_GAUCAUAAUUAUAGAAAUUAUGAAACAC_GCCCC______CACACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCA
............(((((((.....)))))))......................(((((((((....((.....))..)))))))))...........(((((........)))))... (-14.29 = -15.32 +   1.03)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,233,599 – 10,233,714
Length 115
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.44
Mean single sequence MFE -32.54
Consensus MFE -17.72
Energy contribution -19.00
Covariance contribution 1.28
Combinations/Pair 1.15
Mean z-score -1.87
Structure conservation index 0.54
SVM decision value 0.29
SVM RNA-class probability 0.668248
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10233599 115 - 27905053
UGCGCCGGUGGUCCUGCCAGCGAAUUAGCGGUCUGUUAUUAAGCCUGAGUGGUUUAUAAUAACAGUCUGUCCGAUGGGGC-UUGAUUCAUAAUUUCUAUAAUUAUUUGU-GAGCCUG-
..(((.(((......))).))).....((((.(((((((((((((.....))))..))))))))).))))......((((-(((....((((((.....))))))...)-)))))).- ( -35.30)
>DroVir_CAF1 108889 109 - 1
UGCGCUGGUGGUCCUGCCAGCCAAUUAGCGGCCUGUUAUUAAGCGUGAGUGGUUUAUAAUAACAGUGAA-------GGCU-GCGUUUCAUAAUUUCUAUAAUUAUGGUCAGAUAUUU-
((.((((((......))))))))....((((((((((((((.((....))......))))))).....)-------))))-))...((((((((.....))))))))..........- ( -32.90)
>DroGri_CAF1 96540 110 - 1
UGCGCUGGUGGUCCUGCCAGCCAAUUAGCGGCCUGUUAUUAAGCGUGAGUGGUUUAUAAUAACAGUGCA-------GACU-GUAUUUCAUAAUUUCUAUAAUUAUGACUAGAAUUUUU
((.((((((......))))))))..((((.(((((((((((.((....))......))))))))).)).-------).))-)....((((((((.....))))))))........... ( -30.30)
>DroWil_CAF1 105601 112 - 1
UGUGCUGGUGGUCCUGCCAGCCAAUUAGCGACCUGUUAUUAAGCCUGAGUGGUUUAUAAUAAUAGUGUGU-----GUGGCUGAGUUUCAUAAUUUCUAUAAUUAUUAGCAUAGACCG-
((((((((((((...((((((((....(((..(((((((((((((.....))))..)))))))))..)))-----.)))))).))...............)))))))))))).....- ( -33.97)
>DroAna_CAF1 83407 111 - 1
UUCGCCGGUGGUCCUGCCGACCAAUUAGCGGCCUGUUAUUAAGCCUGAGUGGUUUAUAAUAACAGCGUAC----UGGGGC-AUGAUUCAUUAUUUCAAUAAUUAGGCUC-GGACCUG-
..(((..((((((.....)))).))..)))(((((((((((((((.....))))..))))))))).)).(----((((.(-.(((((.(((.....))))))))).)))-)).....- ( -32.10)
>DroPer_CAF1 102858 111 - 1
GGUCUUGGUGGUCCUGCCAGCCAAUUAGUGGACUGUUAUUAAGCCUGAGUGGUUUAUAAUAACAGUGUGG----UCAAGC-AUGACUCAUAAUUUCUAUAAUUAUGACA-GAGUCUG-
.((((((((((.....))).))))...((((((((((((((((((.....))))..)))))))))(((((----(((...-.)))).))))...)))))......))).-.......- ( -30.70)
>consensus
UGCGCUGGUGGUCCUGCCAGCCAAUUAGCGGCCUGUUAUUAAGCCUGAGUGGUUUAUAAUAACAGUGUA______GGGGC_GUGAUUCAUAAUUUCUAUAAUUAUGACC_GAGACUG_
...((((((......))))))...........(((((((((((((.....))))..))))))))).....................((((((((.....))))))))........... (-17.72 = -19.00 +   1.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,233,636 – 10,233,733
Length 97
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 79.75
Mean single sequence MFE -21.25
Consensus MFE -14.33
Energy contribution -14.50
Covariance contribution 0.17
Combinations/Pair 1.19
Mean z-score -1.94
Structure conservation index 0.67
SVM decision value 0.89
SVM RNA-class probability 0.875106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10233636 97 + 27905053
CCCA--UCGGACAGACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGACCGCUAAUUCGCUGGCAGGACCACCGGCGCAUCAAAUCAGGCAUUCA-GCC
....--((((.....(((((((((....((.....))..))))))))).((((((......)))).))....))))............(((.....-))) ( -22.10)
>DroVir_CAF1 108927 90 + 1
CC---------UUCACUGUUAUUAUAAACCACUCACGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCAUCAAAUCAAC-AAGCCUCCC
((---------(...(((((((((...............)))))))))((((((....))).))))))......................-......... ( -17.06)
>DroGri_CAF1 96579 89 + 1
UC---------UGCACUGUUAUUAUAAACCACUCACGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCAUCAAAUCAAC-AUGCC-ACC
((---------(((.(((((((((...............)))))))))((((.....))))..))))).......(.((((.........-)))))-... ( -19.96)
>DroYak_CAF1 97559 99 + 1
CCCACCACGGACAGACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGAUCGCUAAUUGGCUGGCAGGACCACCGGCGCAUCAAAUCAGCCAUUUA-GCC
.((.....))...(((((((((((....((.....))..))))))))).))(((((.((((((((.((....)).)).........)))))).)))-)). ( -29.00)
>DroAna_CAF1 83444 90 + 1
CCCA------GUACGCUGUUAUUAUAAACCACUCAGGCUUAAUAACAGGCCGCUAAUUGGUCGGCAGGACCACCGGCGAAUCAAAUCAGACAUUCA----
....------((...(((((((((....((.....))..)))))))))((((.....(((((.....))))).))))............)).....---- ( -21.80)
>DroPer_CAF1 102895 90 + 1
UUGA------CCACACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGUCCACUAAUUGGCUGGCAGGACCACCAAGACCUCAAAUCAGACAG----ACC
((((------....((((((((((....((.....))..)))))))))).......((((.(((.....)))))))....)))).........----... ( -17.60)
>consensus
CCCA_______CACACUGUUAUUAUAAACCACUCAGGCUUAAUAACAGGCCGCUAAUUGGCUGGCAGGACCACCAGCGCAUCAAAUCAGCCAUUCA_ACC
...............(((((((((....((.....))..)))))))))...........(((((........)))))....................... (-14.33 = -14.50 +   0.17)

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 11:09:37 2006