Locus 6359

Sequence ID 2L_DroMel_CAF1
Location 17,755,495 – 17,755,616
Length 121
Max. P 0.992299
window10160 window10161 window10162 window10163

overview

Window 0

Location 17,755,495 – 17,755,592
Length 97
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 72.82
Mean single sequence MFE -23.87
Consensus MFE -12.09
Energy contribution -13.95
Covariance contribution 1.87
Combinations/Pair 1.21
Mean z-score -1.65
Structure conservation index 0.51
SVM decision value 0.25
SVM RNA-class probability 0.652742
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17755495 97 + 22407834
CUUCUAGUGUUGACUAAGGCCAUUU-----AAAGACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUUAAGCCCUAG--
....(((((((((...((((.....-----.......((((.....---------....))))(((((((((.......)))))))))..)))))))))))))........-- ( -25.60)
>DroSec_CAF1 55469 97 + 1
UUUCUAGUGUUGACUAAGGCCAUUU-----AAAGACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCUACAUAAAGCCCUAG--
.............(((.(((.....-----..(((..(((.(((..---------.....)))(((((((((.......))))))))).)))..))).......))).)))-- ( -21.94)
>DroSim_CAF1 59330 97 + 1
UUUCUAGUGUUGACUAAGGCCAUUU-----AAAAACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCCUAG--
......(((((((...((((.....-----.......((((.....---------....))))(((((((((.......)))))))))..)))))))))))..........-- ( -23.80)
>DroEre_CAF1 64540 97 + 1
GUGCUAGUGUUGGCUAAGGCCAUCU-----AGAGACUGCGUGUAAG---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCUUCG--
...((((...((((....)))).))-----)).((((.......))---------))....(.(((((((((.......))))))))).)(((((......))))).....-- ( -28.50)
>DroYak_CAF1 57775 105 + 1
-UGCUAGUGUUGGCUAAGUCCAUUU-----GAAGACUGCGUUUAAGGAAAAUGCAUUAAAUGCAAAGCCAUGUUUUCCACAAAGCAUUUCGCUUUCAAAAUAAAGCCUUCG--
-.(((.....(((((.((((.....-----...))))((((((((.(......).))))))))..)))))((((((....(((((.....))))).)))))).))).....-- ( -22.80)
>DroAna_CAF1 63325 89 + 1
---------------GAACCCACUUUGCCGUAAGUCAAGCUGUAAG---------CCGGAGGUUGAGCCGUGUUUUCAUCACAGCUUUUCCCAUUUGACACUGCACCUUAGGU
---------------..(((.....(((.((..(((((((.....)---------)..(.((..((((.(((.......))).))))..)))..))))))).))).....))) ( -20.60)
>consensus
_UUCUAGUGUUGACUAAGGCCAUUU_____AAAGACUGCGUGUAAA_________UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCCUAG__
......(((((((...((((................(((((..................)))))((((((((.......))))))))...)))))))))))............ (-12.09 = -13.95 +   1.87)

alignment

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secondary structure

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Window 1

Location 17,755,495 – 17,755,592
Length 97
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 72.82
Mean single sequence MFE -28.80
Consensus MFE -14.13
Energy contribution -13.92
Covariance contribution -0.22
Combinations/Pair 1.44
Mean z-score -2.52
Structure conservation index 0.49
SVM decision value 2.32
SVM RNA-class probability 0.992299
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17755495 97 - 22407834
--CUAGGGCUUAAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUCUUU-----AAAUGGCCUUAGUCAACACUAGAAG
--((((((((...((..((..(((.((((((((((.....)))))))))).....((.---------....)))))..))..)-----)...))))))))............. ( -29.90)
>DroSec_CAF1 55469 97 - 1
--CUAGGGCUUUAUGUAGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUCUUU-----AAAUGGCCUUAGUCAACACUAGAAA
--((((((((......(((..(((.((((((((((.....)))))))))).....((.---------....)))))..)))..-----....))))))))............. ( -31.10)
>DroSim_CAF1 59330 97 - 1
--CUAGGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUUUUU-----AAAUGGCCUUAGUCAACACUAGAAA
--((((((((.....((((((((..((((((((((.....))))))))))((......---------.......)).))))))-----))..))))))))............. ( -31.42)
>DroEre_CAF1 64540 97 - 1
--CGAAGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------CUUACACGCAGUCUCU-----AGAUGGCCUUAGCCAACACUAGCAC
--.((..((.....((..((.((((..((((((((.....)))))))))))).))..)---------)......))..)).((-----((.((((....))))...))))... ( -30.80)
>DroYak_CAF1 57775 105 - 1
--CGAAGGCUUUAUUUUGAAAGCGAAAUGCUUUGUGGAAAACAUGGCUUUGCAUUUAAUGCAUUUUCCUUAAACGCAGUCUUC-----AAAUGGACUUAGCCAACACUAGCA-
--.((((((......(((((.(((((..(((.(((.....))).)))))))).)))))(((.(((.....))).)))))))))-----...(((......))).........- ( -23.00)
>DroAna_CAF1 63325 89 - 1
ACCUAAGGUGCAGUGUCAAAUGGGAAAAGCUGUGAUGAAAACACGGCUCAACCUCCGG---------CUUACAGCUUGACUUACGGCAAAGUGGGUUC---------------
(((((...(((.(((((((..(((...(((((((.(....))))))))...)))...(---------(.....)))))))..)).)))...)))))..--------------- ( -26.60)
>consensus
__CUAAGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA_________CUUACACGCAGUCUUU_____AAAUGGCCUUAGUCAACACUAGAA_
....((((((.................((((((((.....))))))))((((......................))))..............))))))............... (-14.13 = -13.92 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,755,523 – 17,755,616
Length 93
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 77.42
Mean single sequence MFE -23.67
Consensus MFE -13.32
Energy contribution -13.85
Covariance contribution 0.53
Combinations/Pair 1.32
Mean z-score -2.82
Structure conservation index 0.56
SVM decision value 2.07
SVM RNA-class probability 0.987107
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17755523 93 + 22407834
GACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUUAAGCCCUAG-------GCAUUUUCGCUUCACUGUCAUCCA
(((...(((....---------..(((((((((((((((.......)))))))))..((((........)))).....-------))))))......))).)))..... ( -25.00)
>DroSec_CAF1 55497 93 + 1
GACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCUACAUAAAGCCCUAG-------GCAUUUUCGCUUCACUGUCAUCCA
(((...(((....---------..(((((((((((((((.......)))))))))..(((((......))))).....-------))))))......))).)))..... ( -25.30)
>DroSim_CAF1 59358 93 + 1
AACUGCGUGUAAA---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCCUAG-------GCAUUUUCGCUUCACUGUCAUCCA
......(((....---------..(((((((((((((((.......)))))))))..(((((......))))).....-------))))))......)))......... ( -22.50)
>DroEre_CAF1 64568 93 + 1
GACUGCGUGUAAG---------UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCUUCG-------GCAUUUCCACUUCACUGUCAUCCA
(((...(((.(((---------(.(((((((((((((((.......)))))))))..(((((......))))).....-------))))))..))))))).)))..... ( -27.80)
>DroYak_CAF1 57802 102 + 1
GACUGCGUUUAAGGAAAAUGCAUUAAAUGCAAAGCCAUGUUUUCCACAAAGCAUUUCGCUUUCAAAAUAAAGCCUUCG-------GCAUUUUCACUUCACUGUCAUCCA
((((((((((((.(......).)))))))))..((((((((((....)))))))...(((((......)))))....)-------))..............)))..... ( -21.90)
>DroAna_CAF1 63343 100 + 1
GUCAAGCUGUAAG---------CCGGAGGUUGAGCCGUGUUUUCAUCACAGCUUUUCCCAUUUGACACUGCACCUUAGGUCCCACGUAUUCCUCUGUCCCUGUCAACCA
.....((.....)---------).((.((..((((.(((.......))).))))..))...((((((..(((....(((...........))).)))...)))))))). ( -19.50)
>consensus
GACUGCGUGUAAA_________UCAAAUGCAAAGCUGUGCUUUCCACACAGCUUUUCGCUUUCAACAUAAAGCCCUAG_______GCAUUUUCGCUUCACUGUCAUCCA
........................(((((((((((((((.......)))))))))..((((........))))............)))))).................. (-13.32 = -13.85 +   0.53)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,755,523 – 17,755,616
Length 93
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 77.42
Mean single sequence MFE -27.43
Consensus MFE -16.88
Energy contribution -17.08
Covariance contribution 0.20
Combinations/Pair 1.37
Mean z-score -1.98
Structure conservation index 0.62
SVM decision value 1.14
SVM RNA-class probability 0.921082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17755523 93 - 22407834
UGGAUGACAGUGAAGCGAAAAUGC-------CUAGGGCUUAAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUC
.........(((((....((((((-------.....((((........))))..((((((((((.....))))))))))))))))..---------)))))........ ( -26.70)
>DroSec_CAF1 55497 93 - 1
UGGAUGACAGUGAAGCGAAAAUGC-------CUAGGGCUUUAUGUAGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUC
.........(((((....((((((-------.....(((((......)))))..((((((((((.....))))))))))))))))..---------)))))........ ( -27.90)
>DroSim_CAF1 59358 93 - 1
UGGAUGACAGUGAAGCGAAAAUGC-------CUAGGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------UUUACACGCAGUU
.........(((((....((((((-------.....(((((......)))))..((((((((((.....))))))))))))))))..---------)))))........ ( -27.90)
>DroEre_CAF1 64568 93 - 1
UGGAUGACAGUGAAGUGGAAAUGC-------CGAAGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA---------CUUACACGCAGUC
.....(((.(((((((.(((.(((-------.....(((((......)))))..((((((((((.....)))))))))))))))).)---------))).)))...))) ( -30.90)
>DroYak_CAF1 57802 102 - 1
UGGAUGACAGUGAAGUGAAAAUGC-------CGAAGGCUUUAUUUUGAAAGCGAAAUGCUUUGUGGAAAACAUGGCUUUGCAUUUAAUGCAUUUUCCUUAAACGCAGUC
.....(((.((((((.((((((((-------.....(((((......))))).((((((.(..((.....))..)....))))))...)))))))))))...))).))) ( -25.40)
>DroAna_CAF1 63343 100 - 1
UGGUUGACAGGGACAGAGGAAUACGUGGGACCUAAGGUGCAGUGUCAAAUGGGAAAAGCUGUGAUGAAAACACGGCUCAACCUCCGG---------CUUACAGCUUGAC
.((((((......((...((.(((...(.(((...))).).)))))...))......((((((.(....)))))))))))))((.((---------(.....))).)). ( -25.80)
>consensus
UGGAUGACAGUGAAGCGAAAAUGC_______CUAAGGCUUUAUGUUGAAAGCGAAAAGCUGUGUGGAAAGCACAGCUUUGCAUUUGA_________CUUACACGCAGUC
..............(((...................(((((......)))))(.((((((((((.....)))))))))).).....................))).... (-16.88 = -17.08 +   0.20)

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 12:09:12 2006