Locus 3473

Sequence ID 2L_DroMel_CAF1
Location 10,109,305 – 10,109,470
Length 165
Max. P 0.995351
window5487 window5488 window5489 window5490 window5491

overview

Window 7

Location 10,109,305 – 10,109,403
Length 98
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -27.34
Consensus MFE -16.04
Energy contribution -16.44
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.59
SVM decision value 0.04
SVM RNA-class probability 0.555445
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10109305 98 + 22407834
ACACACAC--ACACUUGCAGGCACAGAGAC--UGGAUUCAGGAUUCAGGAAUCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
......((--((....((.((((.(((.((--(((((((.........))))))).)).))))))).))....(((......)))))))............. ( -29.50)
>DroSec_CAF1 35647 78 + 1
ACACACAC--AC-------------GAGAC--UGGAUUCAGGAUU-------CCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
......((--((-------------((..(--((....)))....-------.((((((((..((.....)).))))))))..))))))............. ( -22.10)
>DroSim_CAF1 39098 78 + 1
ACACACAC--AC-------------GAGAC--UGGAUUCAGGAUU-------CCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
......((--((-------------((..(--((....)))....-------.((((((((..((.....)).))))))))..))))))............. ( -22.10)
>DroEre_CAF1 34274 96 + 1
ACACACAC--AU----GCAGGCAUAGAGACCGGGGAUUCAGGAUUCAGGAUUCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
....((((--((----(((((((.(((.(((.(((((((........))))))).))).)))))))((.((....))))))))).))))............. ( -34.70)
>DroYak_CAF1 35752 98 + 1
AUACACACAGAU----ACCGGAUUCAGGAGGCAGGAUUCAGGAUUCAGAAUUCCAGGUGUCUUGCCGACUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
.(((((......----........(((..((((((((.(.(((........)))..).))))))))..)))..(((......))))))))............ ( -28.30)
>consensus
ACACACAC__AC_____C_GG____GAGAC__UGGAUUCAGGAUUCAG_A_UCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAU
..((((...........................(((((...))))).......((((((((..((.....)).))))))))....))))............. (-16.04 = -16.44 +   0.40)

alignment

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secondary structure

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Window 8

Location 10,109,332 – 10,109,438
Length 106
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 83.83
Mean single sequence MFE -29.72
Consensus MFE -23.48
Energy contribution -24.37
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -2.30
Structure conservation index 0.79
SVM decision value 0.69
SVM RNA-class probability 0.823886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10109332 106 + 22407834
C--UGGAUUCAGGAUUCAGGAAUCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGAACACA
(--(((((((.........))))))))((((...((.((.((....)))).)).(((..(((((((((((.....))))))))..(((..-----..))))))..))))))). ( -32.20)
>DroSec_CAF1 35661 99 + 1
C--UGGAUUCAGGAUU-------CCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAAA-----UAUUCGUGUGCGAACACA
(--((((........)-------))))((((...((.((.((....)))).)).(((..(((((((((((.....))))))))..(((..-----..))))))..))))))). ( -28.30)
>DroSim_CAF1 39112 99 + 1
C--UGGAUUCAGGAUU-------CCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGAACACA
(--((((........)-------))))((((...((.((.((....)))).)).(((..(((((((((((.....))))))))..(((..-----..))))))..))))))). ( -28.30)
>DroEre_CAF1 34297 108 + 1
CCGGGGAUUCAGGAUUCAGGAUUCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGAACACA
.(((((((((........)))))))(((((((..((.....)).))))))).))(((..(((((((((((.....))))))))..(((..-----..))))))..)))..... ( -31.60)
>DroYak_CAF1 35777 108 + 1
GGCAGGAUUCAGGAUUCAGAAUUCCAGGUGUCUUGCCGACUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGCACACA
(((.((((((........))))))((((((((..((.....)).)))))))).)))((((((((((((((.....))))))))(((((..-----..)))))))))))..... ( -34.20)
>DroAna_CAF1 38679 92 + 1
-------------------GUUUCCAGGUGUCUUGCCGGCUGUUGACAUCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUACGACAUACACACAUGCCACU--A
-------------------.....((((((((..((.....)).)))))))).(((((((.(((((((((.....))))))))..).)))))))................--. ( -23.70)
>consensus
C__UGGAUUCAGGAUU___GAUUCCAGGUGUCUUGCCGGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA_____UAUUCGUGUGCGAACACA
........................((((((((..((.....)).))))))))..(((..(((((((((((.....))))))))..(((((.....))))))))..)))..... (-23.48 = -24.37 +   0.89)

alignment

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secondary structure

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Window 9

Location 10,109,332 – 10,109,438
Length 106
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 83.83
Mean single sequence MFE -27.12
Consensus MFE -20.94
Energy contribution -21.97
Covariance contribution 1.03
Combinations/Pair 1.04
Mean z-score -2.38
Structure conservation index 0.77
SVM decision value 0.64
SVM RNA-class probability 0.809731
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10109332 106 - 22407834
UGUGUUCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCCGGCAAGACACCUGGAUUCCUGAAUCCUGAAUCCA--G
((((((((....))))))-----))...((((((((((.....)))))))))).........(((((((............)))))))((((((..(....).)))))).--. ( -28.90)
>DroSec_CAF1 35661 99 - 1
UGUGUUCGCACACGAAUA-----UUUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCCGGCAAGACACCUGG-------AAUCCUGAAUCCA--G
.(((((((....))))))-----).(((((((((((((.....))))))))))........((((((((............)))))))))-------))..(((....))--) ( -25.40)
>DroSim_CAF1 39112 99 - 1
UGUGUUCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCCGGCAAGACACCUGG-------AAUCCUGAAUCCA--G
((((((((....))))))-----))(((((((((((((.....))))))))))........((((((((............)))))))))-------))..(((....))--) ( -26.80)
>DroEre_CAF1 34297 108 - 1
UGUGUUCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCCGGCAAGACACCUGGAAUCCUGAAUCCUGAAUCCCCGG
((((((((....))))))-----))(((((((((((((.....)))))))))).((.((..((((((((............))))))))...)).))......)))....... ( -26.90)
>DroYak_CAF1 35777 108 - 1
UGUGUGCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGUCGGCAAGACACCUGGAAUUCUGAAUCCUGAAUCCUGCC
.((((((......(((..-----..)))..((((((((.....))))))))))))))...(((((..(((...(((.....)))....(((........))))))..))))). ( -29.10)
>DroAna_CAF1 38679 92 - 1
U--AGUGGCAUGUGUGUAUGUCGUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGAUGUCAACAGCCGGCAAGACACCUGGAAAC-------------------
.--..((((((.(((((.(((.((((....((((((((.....)))))))))))))))))))).))))))....((((........))))....------------------- ( -25.60)
>consensus
UGUGUUCGCACACGAAUA_____UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCCGGCAAGACACCUGGAAUC___AAUCCUGAAUCCA__G
(((((........(((((.....)))))((((((((((.....)))))))))))))))...((((((((............))))))))........................ (-20.94 = -21.97 +   1.03)

alignment

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secondary structure

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Window 0

Location 10,109,367 – 10,109,470
Length 103
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 74.87
Mean single sequence MFE -22.78
Consensus MFE -8.10
Energy contribution -7.99
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.36
SVM decision value -0.04
SVM RNA-class probability 0.511456
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10109367 103 + 22407834
GGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGAACACAUGCUA-------GUGUGCAUCUUUUUUGUCGCCUCCUUU
(((.....((((..((((.((((..((((((((.....)))))))).......-----...(((....)))))))))))..-------))))(((.......))).)))...... ( -24.70)
>DroPse_CAF1 33057 82 + 1
GGCUGUUGACAUCUGCG-----UACUUCAAUUAAAAUUUAAUUGAAAUACAUA-------------------CAUAUGUCU-------GUGUACAUCCUUUUUGCCGCCUUC--C
(((.((.(((((.((.(-----((.((((((((.....)))))))).)))...-------------------)).)))))(-------(....))........)).)))...--. ( -16.60)
>DroSec_CAF1 35689 103 + 1
GGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAAA-----UAUUCGUGUGCGAACACAUGCUA-------GUGUGCAUCUUUUUUGUCGCCUCCUUC
(((.....((((..((((.((((..((((((((.....)))))))).......-----...(((....)))))))))))..-------))))(((.......))).)))...... ( -24.70)
>DroYak_CAF1 35814 103 + 1
GACUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA-----UAUUCGUGUGCGCACACAUGCUA-------GUGUGCAUCUUUUUUGUCGCCUCCAUC
(((....(((......)))..((((((((((((.....))))))))(((((..-----..)))))))))((((((......-------)))))).........)))......... ( -25.00)
>DroAna_CAF1 38697 111 + 1
GGCUGUUGACAUCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUACGACAUACACACAUGCCACU--AUACUAUGUAUGUAUGUGCAUCUUUUUUGUGGCCUUC--C
(((..(.......((((((((((.(((((((((.....))))))))..).)))))))..(((.((((((....--.......)))))).))))))........)..)))...--. ( -29.06)
>DroPer_CAF1 33069 82 + 1
GGCUGUUGACAUCUGCG-----UACUUCAAUUAAAAUUUAAUUGAAAUACAUA-------------------CAUAUGUCU-------GUGUACAUCCUUUUUGCCGCCUUC--C
(((.((.(((((.((.(-----((.((((((((.....)))))))).)))...-------------------)).)))))(-------(....))........)).)))...--. ( -16.60)
>consensus
GGCUGUUGACACCUGCGUCGUGUACUUCAAUUAAAUUUUAAUUGAAAUGAAUA_____UAUUCGUGUGCGAACACAUGCUA_______GUGUGCAUCUUUUUUGUCGCCUCC__C
(((......................((((((((.....)))))))).............................((((.............))))..........)))...... ( -8.10 =  -7.99 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,109,367 – 10,109,470
Length 103
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.87
Mean single sequence MFE -24.97
Consensus MFE -13.13
Energy contribution -12.35
Covariance contribution -0.77
Combinations/Pair 1.19
Mean z-score -2.82
Structure conservation index 0.53
SVM decision value 2.57
SVM RNA-class probability 0.995351
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10109367 103 - 22407834
AAAGGAGGCGACAAAAAAGAUGCACAC-------UAGCAUGUGUUCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCC
......(((..(......).((.((((-------(.(((((((((((....))))))-----)))..((((((((((.....)))))))))).......)).)))))))...))) ( -25.30)
>DroPse_CAF1 33057 82 - 1
G--GAAGGCGGCAAAAAGGAUGUACAC-------AGACAUAUG-------------------UAUGUAUUUCAAUUAAAUUUUAAUUGAAGUA-----CGCAGAUGUCAACAGCC
.--...(((.(((.......)))....-------.(((((.((-------------------(..((((((((((((.....)))))))))))-----)))).)))))....))) ( -22.90)
>DroSec_CAF1 35689 103 - 1
GAAGGAGGCGACAAAAAAGAUGCACAC-------UAGCAUGUGUUCGCACACGAAUA-----UUUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGCC
......(((..(......).((.((((-------(.((..(((((((....))))))-----)....((((((((((.....)))))))))).......)).)))))))...))) ( -23.10)
>DroYak_CAF1 35814 103 - 1
GAUGGAGGCGACAAAAAAGAUGCACAC-------UAGCAUGUGUGCGCACACGAAUA-----UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGGUGUCAACAGUC
.........((((........((((((-------......))))))((....(((..-----..)))((((((((((.....)))))))))).......))...))))....... ( -24.50)
>DroAna_CAF1 38697 111 - 1
G--GAAGGCCACAAAAAAGAUGCACAUACAUACAUAGUAU--AGUGGCAUGUGUGUAUGUCGUAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGAUGUCAACAGCC
.--...(((.........(((((((((((((((((.((..--....)))))))))))))).))))).((((((((((.....))))))))))....((((....))))....))) ( -31.10)
>DroPer_CAF1 33069 82 - 1
G--GAAGGCGGCAAAAAGGAUGUACAC-------AGACAUAUG-------------------UAUGUAUUUCAAUUAAAUUUUAAUUGAAGUA-----CGCAGAUGUCAACAGCC
.--...(((.(((.......)))....-------.(((((.((-------------------(..((((((((((((.....)))))))))))-----)))).)))))....))) ( -22.90)
>consensus
G__GAAGGCGACAAAAAAGAUGCACAC_______UAGCAUGUGUUCGCACACGAAUA_____UAUUCAUUUCAAUUAAAAUUUAAUUGAAGUACACGACGCAGAUGUCAACAGCC
......(((((((......((((.............))))...........................((((((((((.....))))))))))............))))....))) (-13.13 = -12.35 +  -0.77)

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 10:53:20 2006