Locus 2175

Sequence ID 2R_DroMel_CAF1
Location 8,055,925 – 8,056,056
Length 131
Max. P 0.992008
window3590 window3591 window3592 window3593

overview

Window 0

Location 8,055,925 – 8,056,024
Length 99
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 81.06
Mean single sequence MFE -37.27
Consensus MFE -21.98
Energy contribution -23.26
Covariance contribution 1.28
Combinations/Pair 1.17
Mean z-score -1.83
Structure conservation index 0.59
SVM decision value 0.07
SVM RNA-class probability 0.569187
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8055925 99 + 20766785
CGUGGGCAGGGCGCCAGAUAC----UGUUGUCCACUUUUGCAAUAGCAAGUACAACAGCAAUAGCAA------------CUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
.((.((((((((((((.((((----((((((.....(((((....)))))....))))))...((..------------..)))))).).)))))).....)))))..))..... ( -35.60)
>DroSec_CAF1 20864 99 + 1
CGUGGGCAGGGCGCCAGAUAC----UGUUGUCCAGUUUUGCAAGAGCAACUACAACAGCAAUAGCAA------------AUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
.((.((((((((((((.((((----((((((..(((..(((....))))))))))))(((.......------------.))))))).).)))))).....)))))..))..... ( -35.00)
>DroSim_CAF1 4773 99 + 1
CGUGGGCAGGGCGCCAGAUAC----UGUUGUCCAGUUUUGCAAGAGCAACUACAACAGCAAUAGCAA------------AUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
.((.((((((((((((.((((----((((((..(((..(((....))))))))))))(((.......------------.))))))).).)))))).....)))))..))..... ( -35.00)
>DroEre_CAF1 19114 105 + 1
CGUGGGCAGGGCACCAGAUAC----UGUUGUCCAGUUUUGCAAGAGCGAGUACAACAGCAAUAGCAACAGCAA------CUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
....(((..(((((((.((((----((((((.....(((((....))))).))))))(((...((....))..------.))))))).)))(((.....)))))))..))).... ( -34.90)
>DroYak_CAF1 19049 111 + 1
CGUGGGCAGGGCACCAGAUAC----UGUUGUCCAGUUUUGCAAGAGCAAGUACAACAGCAACAGCAACGGCAAUGGCAUCUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
....(((..(((........(----((((((...(((((((....))))).))....)))))))....(((((((((..(..(....)..)..))).)))))))))..))).... ( -40.50)
>DroAna_CAF1 21258 90 + 1
UGUGGGCUGGAGGCUGGAAGCCCCUUGUCGGCCAGCCGGGCAG-----CCUGCAAC------AGAAU------------CUGCG--UGUGGGCGCCAAUUGCUGCCAGGCCAUAA
(((((.((((.((((((..((.....))...)))))).(((.(-----((..((.(------((...------------)))..--))..))))))........)))).))))). ( -42.60)
>consensus
CGUGGGCAGGGCGCCAGAUAC____UGUUGUCCAGUUUUGCAAGAGCAACUACAACAGCAAUAGCAA____________CUGCGUGUGUGGGCGCCAAUUGCUGCCAGGCCAUAA
....(((..(((((((.((((....((((((......((((....)))).....))))))...(((..............))))))).)))(((.....)))))))..))).... (-21.98 = -23.26 +   1.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,055,925 – 8,056,024
Length 99
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 81.06
Mean single sequence MFE -35.40
Consensus MFE -20.53
Energy contribution -21.26
Covariance contribution 0.73
Combinations/Pair 1.17
Mean z-score -1.86
Structure conservation index 0.58
SVM decision value 0.05
SVM RNA-class probability 0.557857
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8055925 99 - 20766785
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAG------------UUGCUAUUGCUGUUGUACUUGCUAUUGCAAAAGUGGACAACA----GUAUCUGGCGCCCUGCCCACG
.........(((((.....((((((.......((..------------..))...(((((((((((((((....)))..)))..))))))----)))...))))))))))).... ( -34.80)
>DroSec_CAF1 20864 99 - 1
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAU------------UUGCUAUUGCUGUUGUAGUUGCUCUUGCAAAACUGGACAACA----GUAUCUGGCGCCCUGCCCACG
.........(((((.....((((((.......((..------------..))...(((((((((..((((....))))......))))))----)))...))))))))))).... ( -35.50)
>DroSim_CAF1 4773 99 - 1
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAU------------UUGCUAUUGCUGUUGUAGUUGCUCUUGCAAAACUGGACAACA----GUAUCUGGCGCCCUGCCCACG
.........(((((.....((((((.......((..------------..))...(((((((((..((((....))))......))))))----)))...))))))))))).... ( -35.50)
>DroEre_CAF1 19114 105 - 1
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAG------UUGCUGUUGCUAUUGCUGUUGUACUCGCUCUUGCAAAACUGGACAACA----GUAUCUGGUGCCCUGCCCACG
....(((..(((((((((((.((........)))))------)))))...((((.(((((((((....((....))........))))))----)))..)))))))..))).... ( -33.90)
>DroYak_CAF1 19049 111 - 1
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAGAUGCCAUUGCCGUUGCUGUUGCUGUUGUACUUGCUCUUGCAAAACUGGACAACA----GUAUCUGGUGCCCUGCCCACG
.........(((((.....((((((...(((.((((..((....))..)))))))(((((((((..((((....))))......))))))----)))...))))))))))).... ( -36.80)
>DroAna_CAF1 21258 90 - 1
UUAUGGCCUGGCAGCAAUUGGCGCCCACA--CGCAG------------AUUCU------GUUGCAGG-----CUGCCCGGCUGGCCGACAAGGGGCUUCCAGCCUCCAGCCCACA
....((((((.((((((((.(((......--))).)------------))..)------))))))))-----))....((((((((.....))(((.....))).)))))).... ( -35.90)
>consensus
UUAUGGCCUGGCAGCAAUUGGCGCCCACACACGCAG____________UUGCUAUUGCUGUUGUACUUGCUCUUGCAAAACUGGACAACA____GUAUCUGGCGCCCUGCCCACG
.........(((((.....((((((.......(((..............))).......(((((..((((....))))......)))))...........))))))))))).... (-20.53 = -21.26 +   0.73)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,055,961 – 8,056,056
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.49
Mean single sequence MFE -34.10
Consensus MFE -16.38
Energy contribution -17.99
Covariance contribution 1.61
Combinations/Pair 1.14
Mean z-score -2.99
Structure conservation index 0.48
SVM decision value 2.30
SVM RNA-class probability 0.992008
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8055961 95 + 20766785
CAAUAGCAAGUACAACAGCAAUAGCAA------------CUGCGUGUGUGGGCGCCA-----AUUGCUGCCAGGCCAUAA-------AGCCCAAUCCGGGCGAAUGGCUCUG-GAGAAUU
...............(((((((.((..------------(..(....)..)..))..-----)))))))(((((((((..-------.((((.....))))..))))).)))-)...... ( -35.10)
>DroVir_CAF1 3119 98 + 1
CAACAGCAGCCGCAACAUUCGGGCCAA------------AUGCGUGUGGGCAGGCCAUAAAAAUAAUUGACAAAACAAAAAAUAACAAACUUAAUG----CGA------CUGCAAAAAUU
.....((((.((((.......((((..------------.(((......)))))))..........(((......)))................))----)).------))))....... ( -22.00)
>DroSec_CAF1 20900 95 + 1
CAAGAGCAACUACAACAGCAAUAGCAA------------AUGCGUGUGUGGGCGCCA-----AUUGCUGCCAGGCCAUAA-------AGCCCAAUCCGGGCGAAUGGCUCUG-GAGAAUU
(((..((..(((((...(((.......------------.)))...)))))..))..-----.)))((.(((((((((..-------.((((.....))))..))))).)))-))).... ( -34.80)
>DroSim_CAF1 4809 95 + 1
CAAGAGCAACUACAACAGCAAUAGCAA------------AUGCGUGUGUGGGCGCCA-----AUUGCUGCCAGGCCAUAA-------AGCCCAAUCCGGGCGAAUGGCUCUG-GAGAAUU
(((..((..(((((...(((.......------------.)))...)))))..))..-----.)))((.(((((((((..-------.((((.....))))..))))).)))-))).... ( -34.80)
>DroEre_CAF1 19150 101 + 1
CAAGAGCGAGUACAACAGCAAUAGCAACAGCAA------CUGCGUGUGUGGGCGCCA-----AUUGCUGCCAGGCCAUAA-------AGCCCAAUCCGGGCGAAUGGCUCUG-GAGAAUU
(((..(((..((((...(((...((....))..------.)))...))))..)))..-----.)))((.(((((((((..-------.((((.....))))..))))).)))-))).... ( -37.10)
>DroYak_CAF1 19085 107 + 1
CAAGAGCAAGUACAACAGCAACAGCAACGGCAAUGGCAUCUGCGUGUGUGGGCGCCA-----AUUGCUGCCAGGCCAUAA-------AGCCCAAUCCGGGCGAAUGGCUCUG-GAGAAUU
.................((....))..((((((((((..(..(....)..)..))).-----)))))))(((((((((..-------.((((.....))))..))))).)))-)...... ( -40.80)
>consensus
CAAGAGCAACUACAACAGCAAUAGCAA____________AUGCGUGUGUGGGCGCCA_____AUUGCUGCCAGGCCAUAA_______AGCCCAAUCCGGGCGAAUGGCUCUG_GAGAAUU
..(((((........((((((..(((..............)))((((....))))........))))))...................((((.....)))).....)))))......... (-16.38 = -17.99 +   1.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,055,961 – 8,056,056
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.49
Mean single sequence MFE -32.18
Consensus MFE -16.44
Energy contribution -17.67
Covariance contribution 1.23
Combinations/Pair 1.22
Mean z-score -1.93
Structure conservation index 0.51
SVM decision value 0.49
SVM RNA-class probability 0.755453
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8055961 95 - 20766785
AAUUCUC-CAGAGCCAUUCGCCCGGAUUGGGCU-------UUAUGGCCUGGCAGCAAU-----UGGCGCCCACACACGCAG------------UUGCUAUUGCUGUUGUACUUGCUAUUG
(((((((-(((.(((((..((((.....)))).-------..))))))))).)).)))-----)((((...(((((.((((------------(....))))))).)))...)))).... ( -32.20)
>DroVir_CAF1 3119 98 - 1
AAUUUUUGCAG------UCG----CAUUAAGUUUGUUAUUUUUUGUUUUGUCAAUUAUUUUUAUGGCCUGCCCACACGCAU------------UUGGCCCGAAUGUUGCGGCUGCUGUUG
.......((((------(((----((....(((((.......(((......)))..........(((((((......))).------------..)))))))))..)))))))))..... ( -26.90)
>DroSec_CAF1 20900 95 - 1
AAUUCUC-CAGAGCCAUUCGCCCGGAUUGGGCU-------UUAUGGCCUGGCAGCAAU-----UGGCGCCCACACACGCAU------------UUGCUAUUGCUGUUGUAGUUGCUCUUG
......(-(((.(((((..((((.....)))).-------..))))))))).((((((-----(((((........)))..------------..((....)).....)))))))).... ( -31.90)
>DroSim_CAF1 4809 95 - 1
AAUUCUC-CAGAGCCAUUCGCCCGGAUUGGGCU-------UUAUGGCCUGGCAGCAAU-----UGGCGCCCACACACGCAU------------UUGCUAUUGCUGUUGUAGUUGCUCUUG
......(-(((.(((((..((((.....)))).-------..))))))))).((((((-----(((((........)))..------------..((....)).....)))))))).... ( -31.90)
>DroEre_CAF1 19150 101 - 1
AAUUCUC-CAGAGCCAUUCGCCCGGAUUGGGCU-------UUAUGGCCUGGCAGCAAU-----UGGCGCCCACACACGCAG------UUGCUGUUGCUAUUGCUGUUGUACUCGCUCUUG
(((((((-(((.(((((..((((.....)))).-------..))))))))).)).)))-----)((((...(((((.((((------(.((....)).))))))).)))...)))).... ( -36.80)
>DroYak_CAF1 19085 107 - 1
AAUUCUC-CAGAGCCAUUCGCCCGGAUUGGGCU-------UUAUGGCCUGGCAGCAAU-----UGGCGCCCACACACGCAGAUGCCAUUGCCGUUGCUGUUGCUGUUGUACUUGCUCUUG
......(-(((.(((((..((((.....)))).-------..)))))))))(((((((-----.(((((........)).(....)...)))))))))).(((....))).......... ( -33.40)
>consensus
AAUUCUC_CAGAGCCAUUCGCCCGGAUUGGGCU_______UUAUGGCCUGGCAGCAAU_____UGGCGCCCACACACGCAG____________UUGCUAUUGCUGUUGUACUUGCUCUUG
........(((.(((((..((((.....))))..........))))))))((((((((.......(((........)))...................)))))))).............. (-16.44 = -17.67 +   1.23)

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 10:23:07 2006