Locus 5340

Sequence ID	2L_DroMel_CAF1
Location	15,122,041 – 15,122,161
Length	120
Max. P	0.988736

overview

Window 0

Location	15,122,041 – 15,122,144
Length	103
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	79.26
Mean single sequence MFE	-33.28
Consensus MFE	-16.83
Energy contribution	-17.25
Covariance contribution	0.42
Combinations/Pair	1.19
Mean z-score	-3.68
Structure conservation index	0.51
SVM decision value	2.13
SVM RNA-class probability	0.988736
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15122041 103 + 22407834
A----AAG--AUG-AACGG--CCAAAG-----GAAAAGCCGAAAGCAGAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGAGCUUGAAGGCCGA
.----...--...-..(((--((....-----......((((((((((..((((.........))))...)))))))))).(((((...(((.....)))....)))))..))))). ( -33.00)
>DroVir_CAF1 93393 104 + 1
ACGGG-------GAAAGAGGGCGGACAGA-----AUGGCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGCCAGUCGGCCCUCAAAAGCGUUGAAC-UGAAGGCUAA
.....-------....((((((.(((...-----.(((((((((((((..((((.........))))...)))))))))))))))).))))))...(((.((....-..)).))).. ( -43.70)
>DroPse_CAF1 83954 106 + 1
A----AAG--ACG-AACGG--CCAAAG--AAGAAAAAGCCGAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGGGCUUGAAGGCCGA
.----...--...-..(((--((....--.........((((((((((..((((.........))))...)))))))))).(((((..(((.(......).))))))))..))))). ( -32.30)
>DroGri_CAF1 82863 110 + 1
ACGG-ACG--GUG-CACGGA-CGGA-CGGUAUAGAAAGCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGGCCCUCAAAAGCGUUAUAC-UGAUGGCUAA
.((.-.((--...-..))..-))..-((((((((...((.((((((((..((((.........))))...))))))))((((.....))))......)).))))))-))........ ( -31.70)
>DroWil_CAF1 128269 105 + 1
A----AAGAUAUG-AACGG--CGCAAA-----AGAAAGCCAAAAGUAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGGCCGUCAAAAGCGUUCAGCUCGAAGGCUGA
.----......((-(.(((--(((...-----.(....((((((((((..((((.........))))...)))))))))).)..)).))))))).......((((((....)))))) ( -28.30)
>DroPer_CAF1 85052 106 + 1
A----AAG--ACG-AACGG--CCAAAG--AAGAAAAAGCCGAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGGGCUUAAAGGCCGA
.----...--...-..(((--((....--.........((((((((((..((((.........))))...))))))))))...(((....)))..((((.....))))...))))). ( -30.70)
>consensus
A____AAG__AUG_AACGG__CCAAAG_____AAAAAGCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGAGCUUGAAGGCCGA
................(((..................(((((((((((..((((.........))))...)))))))))).)......((.(((..(((.....)))))).))))). (-16.83 = -17.25 +   0.42)

alignment

secondary structure

dotplot

Window 1

Location	15,122,041 – 15,122,144
Length	103
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	79.26
Mean single sequence MFE	-25.96
Consensus MFE	-15.56
Energy contribution	-15.67
Covariance contribution	0.11
Combinations/Pair	1.18
Mean z-score	-2.39
Structure conservation index	0.60
SVM decision value	1.21
SVM RNA-class probability	0.930713
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15122041 103 - 22407834
UCGGCCUUCAAGCUCAACGCUUUUGACGGUCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUCUGCUUUCGGCUUUUC-----CUUUGG--CCGUU-CAU--CUU----U
..((((.((((((.....)))..))).))))((..((....((((((.........))))))....))...))...(((((....-----....))--)))..-...--...----. ( -22.70)
>DroVir_CAF1 93393 104 - 1
UUAGCCUUCA-GUUCAACGCUUUUGAGGGCCGACUGGCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGCCAU-----UCUGUCCGCCCUCUUUC-------CCCGU
..........-.....(((.....((((((.((((((((((((((((.((..(((.....)))..))..))))))))))))).-----...))).))))))....-------..))) ( -37.70)
>DroPse_CAF1 83954 106 - 1
UCGGCCUUCAAGCCCAACGCUUUUGACGGUCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUCGGCUUUUUCUU--CUUUGG--CCGUU-CGU--CUU----U
.(((((...(((((....(((((((..(((.....))))))))))...................((((...))))..)))))......--....))--)))..-...--...----. ( -23.82)
>DroGri_CAF1 82863 110 - 1
UUAGCCAUCA-GUAUAACGCUUUUGAGGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGCUUUCUAUACCG-UCCG-UCCGUG-CAC--CGU-CCGU
..(((((..(-(((....((((....((((.....))))..((((((.........))))))..))))..))))..)))))..........-..((-..((..-...--)).-.)). ( -24.70)
>DroWil_CAF1 128269 105 - 1
UCAGCCUUCGAGCUGAACGCUUUUGACGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUACUUUUGGCUUUCU-----UUUGCG--CCGUU-CAUAUCUU----U
(((((......)))))........((((((.((........((((((.........))))))..(((((........)))))...-----...)))--)))))-........----. ( -22.30)
>DroPer_CAF1 85052 106 - 1
UCGGCCUUUAAGCCCAACGCUUUUGACGGUCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUCGGCUUUUUCUU--CUUUGG--CCGUU-CGU--CUU----U
.(((((...(((((....(((((((..(((.....))))))))))...................((((...))))..)))))......--....))--)))..-...--...----. ( -24.52)
>consensus
UCAGCCUUCAAGCUCAACGCUUUUGACGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUCGGCUUUUU_____CUUUCG__CCGUU_CAU__CUU____U
..((((...((((.....(((((((..(((.....))))))))))..........((((....))))....))))..)))).................................... (-15.56 = -15.67 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	15,122,064 – 15,122,161
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.78
Mean single sequence MFE	-31.15
Consensus MFE	-17.03
Energy contribution	-17.20
Covariance contribution	0.17
Combinations/Pair	1.19
Mean z-score	-2.57
Structure conservation index	0.55
SVM decision value	1.62
SVM RNA-class probability	0.968135
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15122064 97 + 22407834
GCCGAAAGCAGAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGAGCUUGAAGGCCGAACAAAUGGCCAGAACAG-----------------------
.((((((((((..((((.........))))...)))))))))).(((((...(((.....)))....)))))..(((((......))))).......----------------------- ( -29.40)
>DroVir_CAF1 93418 95 + 1
GCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGCCAGUCGGCCCUCAAAAGCGUUGAAC-UGAAGGCUAAGCCAAUGGGCGUA---------------GC---------G
(((((((((((..((((.........))))...)))))))))))((((((((.((....)).)))).))-))...((((.(((....))).))---------------))---------. ( -34.50)
>DroGri_CAF1 82894 119 + 1
GCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGGCCCUCAAAAGCGUUAUAC-UGAUGGCUAAGCCAAUGGGCACAUCAGAUCUGAGCGGAGCGAGCGCGGUG
(((((((((((..((((.........))))...))))))))((((.....))))......(((((...(-(((((.....(((....))).)))))).(((....)))...)))))))). ( -37.00)
>DroWil_CAF1 128294 94 + 1
GCCAAAAGUAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGGCCGUCAAAAGCGUUCAGCUCGAAGGCUGAACAAAUGCCCAAAA--------------------------
...((((((((..((((.........))))...))))))))((((((((....)))......((((((((....))))))))...)))))....-------------------------- ( -30.40)
>DroMoj_CAF1 93620 94 + 1
GCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUCGGCUAGGCGGCCCUCAAAAGCGUUGAAC-UGAAGGCUAAGCCAAUGGGCGUG---------------GC----------
(((((((((((..((((.........))))...)))))))((.((((((((((.(((............-))).))))..)))..))).))))---------------))---------- ( -26.10)
>DroPer_CAF1 85078 97 + 1
GCCGAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGACCGUCAAAAGCGUUGGGCUUAAAGGCCGAACAAAUGGCCAGAACGG-----------------------
.((((((((((..((((.........))))...))))))))))........(((((..((((.....))))...(((((......))))).).))))----------------------- ( -29.50)
>consensus
GCCAAAAGCAAAGCUUGUAAACAAAUUAAGAGAUUGCUUUUGGGCAGGCGGCCCUCAAAAGCGUUGAAC_UGAAGGCUAAACAAAUGGCCAGAA__________________________
.((((((((((..((((.........))))...))))))))))......((((.(((.............))).)))).......................................... (-17.03 = -17.20 +   0.17)

alignment

secondary structure

dotplot

Window 3

Location	15,122,064 – 15,122,161
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.78
Mean single sequence MFE	-27.38
Consensus MFE	-15.43
Energy contribution	-15.27
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-2.02
Structure conservation index	0.56
SVM decision value	0.84
SVM RNA-class probability	0.864401
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15122064 97 - 22407834
-----------------------CUGUUCUGGCCAUUUGUUCGGCCUUCAAGCUCAACGCUUUUGACGGUCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUCUGCUUUCGGC
-----------------------.......((((........))))...((((.....(((((((..(((.....))))))))))..........((((....))))....))))..... ( -19.90)
>DroVir_CAF1 93418 95 - 1
C---------GC---------------UACGCCCAUUGGCUUAGCCUUCA-GUUCAACGCUUUUGAGGGCCGACUGGCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGC
.---------((---------------((.(((....))).))))...((-(((....((((....)))).)))))(((((((((((.((..(((.....)))..))..))))))))))) ( -30.50)
>DroGri_CAF1 82894 119 - 1
CACCGCGCUCGCUCCGCUCAGAUCUGAUGUGCCCAUUGGCUUAGCCAUCA-GUAUAACGCUUUUGAGGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGC
......((..((.((.((((((..((.(((((....((((...))))...-))))).))..))))))))..))..))((((((((((.((..(((.....)))..))..)))))))))). ( -34.60)
>DroWil_CAF1 128294 94 - 1
--------------------------UUUUGGGCAUUUGUUCAGCCUUCGAGCUGAACGCUUUUGACGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUACUUUUGGC
--------------------------..(((((((...(((((((......)))))))(((......)))....)))))))((((((.........))))))....(((........))) ( -26.00)
>DroMoj_CAF1 93620 94 - 1
----------GC---------------CACGCCCAUUGGCUUAGCCUUCA-GUUCAACGCUUUUGAGGGCCGCCUAGCCGAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGC
----------((---------------((.......))))...(((((((-(..........))))))))......(((((((((((.((..(((.....)))..))..))))))))))) ( -30.00)
>DroPer_CAF1 85078 97 - 1
-----------------------CCGUUCUGGCCAUUUGUUCGGCCUUUAAGCCCAACGCUUUUGACGGUCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUCGGC
-----------------------(((((..((((........))))...((((.....))))..)))))......(((..(((((((.((..(((.....)))..))..))))))).))) ( -23.30)
>consensus
__________________________UUAUGCCCAUUGGCUCAGCCUUCA_GCUCAACGCUUUUGACGGCCGCCUGCCCAAAAGCAAUCUCUUAAUUUGUUUACAAGCUUUGCUUUUGGC
...........................................(((.(((.((.....))...))).))).......((((((((((.((..(((.....)))..))..)))))))))). (-15.43 = -15.27 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:47 2006