Locus 4389

Sequence ID 2R_DroMel_CAF1
Location 14,432,963 – 14,433,092
Length 129
Max. P 0.995811
window7017 window7018 window7019 window7020

overview

Window 7

Location 14,432,963 – 14,433,071
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.55
Mean single sequence MFE -21.50
Consensus MFE -10.10
Energy contribution -9.60
Covariance contribution -0.50
Combinations/Pair 1.21
Mean z-score -1.98
Structure conservation index 0.47
SVM decision value 1.11
SVM RNA-class probability 0.916776
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14432963 108 + 20766785
UUGUU----------GAUUUUUUGGUUUGGUCUGGUGUGUAAAUUCAUGAAU-UUAUUCAUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGCUGUUUGUCAUUAAUCU
....(----------(((....((((........(((.(((((((....)))-)))).)))(((-((((.((.(.((.....)).).)).))))))).....))))...))))....... ( -22.90)
>DroVir_CAF1 85177 86 + 1
--GUU----------UAUUGUU-G-------UUGUUGCGUAAAUUCAU-------------GCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCGUUUGUCAUUAAUCU
--...----------....(((-(-------.((..((((((((...(-------------(((-((((.((.(.((.....)).).)).))))))))))))).)))....)).)))).. ( -19.70)
>DroGri_CAF1 82309 83 + 1
-----------------------------------UGUGUAAAUUAAUGCAU-UUAUUCAUGCG-CUCAUUGCCUCAAUUAAUUCGGCAUUGAGCGCAAUUUGUCAUUUGUCAUUAAUCU
-----------------------------------.......(((((((((.-.....((((((-((((.((((...........)))).))))))))...)).....)).))))))).. ( -24.80)
>DroWil_CAF1 115771 110 + 1
AUGUUAAUUUGUUUUUAUUUUUUAUUU---------UUGUAAACUCAUGCAU-UUAUUCAAGCACCUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUUGUUUGUCAUUAAUCU
..((((((...................---------.((((......)))).-.....((((((.(..(((((((((((.........)))))).)))))..).))))))..)))))).. ( -17.40)
>DroMoj_CAF1 106840 97 + 1
----U----------GCCCGUU-G-------UUGUUGUAUAAAUUCAUGCAUCUUAUAUGUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCAGUUGUCAUUAAUCU
----.----------.......-.-------...........(((.(((((.((.(((..((((-((((.((.(.((.....)).).)).))))))))...))).)).)).))).))).. ( -20.20)
>DroAna_CAF1 75818 95 + 1
----------------GCUUUU------UGUUUGGCGUGUAAAUUCAUGAAU-GUAUUCAUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGGGCGCAAUUUGCUGU-UGUCAUUAAUCU
----------------......------....(((((.(((((((.(((((.-...)))))(((-((((.((.(.((.....)).).)).))))))))))))))...-)))))....... ( -24.00)
>consensus
____U___________AUUUUU_G_______UUG_UGUGUAAAUUCAUGCAU_UUAUUCAUGCG_CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCGUUUGUCAUUAAUCU
.............................................................(((....(((((((((((.........)))))).))))).)))................ (-10.10 =  -9.60 +  -0.50)

alignment

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secondary structure

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Window 8

Location 14,432,963 – 14,433,071
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 71.55
Mean single sequence MFE -21.70
Consensus MFE -14.81
Energy contribution -15.23
Covariance contribution 0.42
Combinations/Pair 1.14
Mean z-score -3.18
Structure conservation index 0.68
SVM decision value 2.62
SVM RNA-class probability 0.995811
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14432963 108 - 20766785
AGAUUAAUGACAAACAGCAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCAUGAAUAA-AUUCAUGAAUUUACACACCAGACCAAACCAAAAAAUC----------AACAA
.((((.................((((((((.((((.((.....)).)))).))))-))))((..(((-(((....))))))..))................))))----------..... ( -23.70)
>DroVir_CAF1 85177 86 - 1
AGAUUAAUGACAAACGACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGC-------------AUGAAUUUACGCAACAA-------C-AACAAUA----------AAC--
......................((((((((.((((.((.....)).)))).))))-)))-------------)................-------.-.......----------...-- ( -20.30)
>DroGri_CAF1 82309 83 - 1
AGAUUAAUGACAAAUGACAAAUUGCGCUCAAUGCCGAAUUAAUUGAGGCAAUGAG-CGCAUGAAUAA-AUGCAUUAAUUUACACA-----------------------------------
(((((((((.((..........((((((((.((((...........)))).))))-)))).......-.))))))))))).....----------------------------------- ( -26.97)
>DroWil_CAF1 115771 110 - 1
AGAUUAAUGACAAACAACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAGGUGCUUGAAUAA-AUGCAUGAGUUUACAA---------AAAUAAAAAAUAAAAACAAAUUAACAU
...........((((..(..(((((.((((((.........)))))))))))..)((((........-..))))..))))....---------........................... ( -16.20)
>DroMoj_CAF1 106840 97 - 1
AGAUUAAUGACAACUGACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCACAUAUAAGAUGCAUGAAUUUAUACAACAA-------C-AACGGGC----------A----
(((((.(((.((.((.......((((((((.((((.((.....)).)))).))))-))))......)).))))).))))).........-------.-.......----------.---- ( -24.72)
>DroAna_CAF1 75818 95 - 1
AGAUUAAUGACA-ACAGCAAAUUGCGCCCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCAUGAAUAC-AUUCAUGAAUUUACACGCCAAACA------AAAAGC----------------
............-...((.....((((.((.((((.((.....)).)))).)).)-)))(((((...-.)))))..........))......------......---------------- ( -18.30)
>consensus
AGAUUAAUGACAAACAACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG_CGCAUGAAUAA_AUGCAUGAAUUUACACA_CAA_______C_AAAAAU___________A____
(((((.(((.............((((((((.((((.((.....)).)))).)))).))))...........))).)))))........................................ (-14.81 = -15.23 +   0.42)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,432,993 – 14,433,092
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.70
Mean single sequence MFE -20.19
Consensus MFE -10.10
Energy contribution -9.60
Covariance contribution -0.50
Combinations/Pair 1.21
Mean z-score -1.92
Structure conservation index 0.50
SVM decision value 0.33
SVM RNA-class probability 0.693334
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14432993 99 + 20766785
AAAUUCAUGAAU-UUAUUCAUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGCUGUUUGUCAUUAAUCUUCUUUU--CA--------------GUUUUUGGUUA---CG
......(((((.-...)))))(((-((((.((.(.((.....)).).)).)))))))((((.((((....................--))--------------))....)))).---.. ( -17.45)
>DroVir_CAF1 85197 85 + 1
AAAUUCAU-------------GCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCGUUUGUCAUUAAUCUUCUUUU--CA--------------UUU--UCAUUU---GG
.......(-------------(((-((((.((.(.((.....)).).)).))))))))............................--..--------------...--......---.. ( -15.80)
>DroGri_CAF1 82314 99 + 1
AAAUUAAUGCAU-UUAUUCAUGCG-CUCAUUGCCUCAAUUAAUUCGGCAUUGAGCGCAAUUUGUCAUUUGUCAUUAAUCUUCUUUUUUCA--------------UUU--UCACUU---GG
..(((((((((.-.....((((((-((((.((((...........)))).))))))))...)).....)).)))))))............--------------...--......---.. ( -24.80)
>DroWil_CAF1 115802 103 + 1
AAACUCAUGCAU-UUAUUCAAGCACCUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUUGUUUGUCAUUAAUCUUCUUAA--GC--------------AUUUUUCUUUGUCUCU
......((((..-.....((((((.(..(((((((((((.........)))))).)))))..).))))))...((((.....))))--))--------------)).............. ( -18.10)
>DroMoj_CAF1 106858 100 + 1
AAAUUCAUGCAUCUUAUAUGUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCAGUUGUCAUUAAUCUUCUUUG--CA--------------AUUUGUGAUUU---GG
..(((.(((((.((.(((..((((-((((.((.(.((.....)).).)).))))))))...))).)).)).))).))).....(..--(.--------------....)..)...---.. ( -20.60)
>DroAna_CAF1 75836 110 + 1
AAAUUCAUGAAU-GUAUUCAUGCG-CUCAUUGCCUCAAUUAAUGCGACAUUGGGCGCAAUUUGCUGU-UGUCAUUAAUCUUCCUUU--CAAGCCGCAAGACUUGGUUUUUGGUUU-----
..(((.((((..-(((....((((-((((.((.(.((.....)).).)).))))))))...)))...-..)))).)))...((..(--((((.(....).))))).....))...----- ( -24.40)
>consensus
AAAUUCAUGCAU_UUAUUCAUGCG_CUCAUUGCCUCAAUUAAUGCGACAUUGAGCGCAAUUUGUCGUUUGUCAUUAAUCUUCUUUU__CA______________AUUUUUCAUUU___GG
.....................(((....(((((((((((.........)))))).))))).)))........................................................ (-10.10 =  -9.60 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,432,993 – 14,433,092
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.70
Mean single sequence MFE -22.82
Consensus MFE -14.41
Energy contribution -14.83
Covariance contribution 0.42
Combinations/Pair 1.14
Mean z-score -2.90
Structure conservation index 0.63
SVM decision value 2.32
SVM RNA-class probability 0.992376
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14432993 99 - 20766785
CG---UAACCAAAAAC--------------UG--AAAAGAAGAUUAAUGACAAACAGCAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCAUGAAUAA-AUUCAUGAAUUU
..---..........(--------------(.--...)).(((((.((((.......((...((((((((.((((.((.....)).)))).))))-)))))).....-..)))).))))) ( -24.04)
>DroVir_CAF1 85197 85 - 1
CC---AAAUGA--AAA--------------UG--AAAAGAAGAUUAAUGACAAACGACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGC-------------AUGAAUUU
..---......--...--------------..--............................((((((((.((((.((.....)).)))).))))-)))-------------)....... ( -20.30)
>DroGri_CAF1 82314 99 - 1
CC---AAGUGA--AAA--------------UGAAAAAAGAAGAUUAAUGACAAAUGACAAAUUGCGCUCAAUGCCGAAUUAAUUGAGGCAAUGAG-CGCAUGAAUAA-AUGCAUUAAUUU
..---......--...--------------..........(((((((((.((..........((((((((.((((...........)))).))))-)))).......-.))))))))))) ( -26.57)
>DroWil_CAF1 115802 103 - 1
AGAGACAAAGAAAAAU--------------GC--UUAAGAAGAUUAAUGACAAACAACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAGGUGCUUGAAUAA-AUGCAUGAGUUU
................--------------((--(((...........((((...................))))(((((.(((.(((((......))))).))).)-)))).))))).. ( -17.51)
>DroMoj_CAF1 106858 100 - 1
CC---AAAUCACAAAU--------------UG--CAAAGAAGAUUAAUGACAACUGACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCACAUAUAAGAUGCAUGAAUUU
..---...........--------------..--......(((((.(((.((.((.......((((((((.((((.((.....)).)))).))))-))))......)).))))).))))) ( -24.32)
>DroAna_CAF1 75836 110 - 1
-----AAACCAAAAACCAAGUCUUGCGGCUUG--AAAGGAAGAUUAAUGACA-ACAGCAAAUUGCGCCCAAUGUCGCAUUAAUUGAGGCAAUGAG-CGCAUGAAUAC-AUUCAUGAAUUU
-----...........((((((....))))))--......(((((.((((..-.........(((((.((.((((.((.....)).)))).)).)-)))).......-..)))).))))) ( -24.15)
>consensus
CC___AAAUCAAAAAA______________UG__AAAAGAAGAUUAAUGACAAACAACAAAUUGCGCUCAAUGUCGCAUUAAUUGAGGCAAUGAG_CGCAUGAAUAA_AUGCAUGAAUUU
........................................(((((.(((.............((((((((.((((.((.....)).)))).)))).))))...........))).))))) (-14.41 = -14.83 +   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 11:18:27 2006