Locus 544

Sequence ID 2R_DroMel_CAF1
Location 2,862,013 – 2,862,234
Length 221
Max. P 0.745862
window1012 window1013 window1014 window1015

overview

Window 2

Location 2,862,013 – 2,862,133
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.55
Mean single sequence MFE -30.32
Consensus MFE -18.74
Energy contribution -20.77
Covariance contribution 2.03
Combinations/Pair 1.30
Mean z-score -1.51
Structure conservation index 0.62
SVM decision value 0.22
SVM RNA-class probability 0.641333
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2862013 120 - 20766785
AAAACAAUCUUAAGUUUCCAAAUUUAUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCAAAGAUUUCCAGUCUACUCGGCUCGAGUUCGAGUGAUAUUG
..................(((..((((((((((((...(((((.(((((((..((((......)))).((....)).............)))))))..)))))))))))))))))..))) ( -36.10)
>DroSec_CAF1 13646 120 - 1
AAAACACUCCUAAGUUUCCAAAUUUGUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCAAAGAUUUCCAGUCUACUCGGCUCGAGUUCGAGUAAUAUAG
.......................((((((((((((...(((((.(((((((..((((......)))).((....)).............)))))))..)))))))))))))))))..... ( -32.70)
>DroSim_CAF1 20341 120 - 1
AAAACCAUCCUAAGUUUCAAAAUUGAUUUGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCUAAGAUUUCCAGUCUACUCGGCUCGAGUUCGAGUGAUAUAG
.......................(.((((((((((...(((((.(((((((..((((......)))).((....)).............)))))))..))))))))))))))).)..... ( -31.80)
>DroEre_CAF1 13240 114 - 1
AAAACUCUCCUAAGU-CUUGA-----UUCCAACUUUCAGAGCCCGUGGGCUCCAAAGCUCCCACCUUUGCUACGGCUUCAAAGAUUUCCAGCACACUGGGCUCAAGCUCGAGCGAUAUUG
...........((((-(((((-----..((........(((((....)))))(((((.......)))))....))..)).)))))))((((....))))((((......))))....... ( -29.80)
>DroYak_CAF1 15459 119 - 1
AAAACACUCCCAGUU-CUUAAAUUUAUUUAAUGUUCCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCAAAGAUUUCAAGUAUGCUCGACUCAAGUUCGAGUGAUAUUG
....(((((..(((.-(((((((((.............(((((....))))).((((......)))).((....)).....)))))).)))...))).(((....))).)))))...... ( -24.40)
>DroPer_CAF1 13691 103 - 1
AAAAGUA----------------UUGUUUG-AUUUGCAGAACCCGUUGGGGCCAAGGCGCCCACAUUUGCCAGUGUCUCGAAAAUAUCCAGUCUACUCGGCUCCAGUUCGAGUGAUAUUG
...((((----------------(..((((-(.(((........((.(((((....)).)))))....(((((((.((.((.....)).)).).))).)))..))).)))))..))))). ( -27.10)
>consensus
AAAACAAUCCUAAGU_UCCAAAUUUAUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCAAAGAUUUCCAGUCUACUCGGCUCGAGUUCGAGUGAUAUUG
.......................((((((((((((...(((((.(((((((..((((......)))).((....)).............)))))))..)))))))))))))))))..... (-18.74 = -20.77 +   2.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,862,053 – 2,862,165
Length 112
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 72.96
Mean single sequence MFE -31.29
Consensus MFE -16.85
Energy contribution -17.00
Covariance contribution 0.15
Combinations/Pair 1.50
Mean z-score -1.62
Structure conservation index 0.54
SVM decision value 0.41
SVM RNA-class probability 0.726000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2862053 112 + 20766785
UGAAGCCGUAGCAAAGGUUGGAGCCUUGGAGCCCACGGGCUCUGAAAGUUCGAAUAAAUUUGGAAACUUAAGAUUGUUUUGAGG-GUCGCUUAAU----UAACUGCUUGAAUAGGUU
(.((((.((..((((.(((.((((.(..(((((....)))))..)..)))).)))...))))((..(((((((...))))))).-.)).......----..)).)))).)....... ( -32.20)
>DroGri_CAF1 14303 110 + 1
UGAGACACUAGCAAAUGUGGGCGCUUUGGCACCGACGGGUUCUGGAAUUUG-AGUG-AGAGAU--AGUCACAAUUCGUUAGAAAACUAUA--UAAUUGAUAACUGUCUGAAU-GUUA
...((((((((.(..(((.((.((....)).)).)))..).))))......-....-..((((--(((..(((((...(((....)))..--.)))))...)))))))...)-))). ( -25.10)
>DroSec_CAF1 13686 112 + 1
UGAAGCCGUAGCAAAGGUUGGAGCCUUGGAGCCCACGGGCUCUGAAAGUUCGAACAAAUUUGGAAACUUAGGAGUGUUUUGAGG-GACAAAUUUU----AAACUGCCUGAAUAGGUU
...((((....((((.(((.((((.(..(((((....)))))..)..)))).)))...)))).....(((((...((((.(((.-......))).----))))..)))))...)))) ( -33.00)
>DroSim_CAF1 20381 112 + 1
AGAAGCCGUAGCAAAGGUUGGAGCCUUGGAGCCCACGGGCUCUGAAAGUUCAAAUCAAUUUUGAAACUUAGGAUGGUUUUGAGG-GACGAUUAUU----AAACUGCCUGAAUAGGUU
...((((.......((((.(((((.(..(((((....)))))..)..)))).((((..(((..(((((......)))))..)))-...))))...----...).)))).....)))) ( -32.60)
>DroEre_CAF1 13280 106 + 1
UGAAGCCGUAGCAAAGGUGGGAGCUUUGGAGCCCACGGGCUCUGAAAGUUGGAA-----UCAAG-ACUUAGGAGAGUUUUGAGG-GACGAUUGUU----AAACUGCCUGAGUGGGUG
....(((...((..(((..(.(((((..(((((....)))))..))(((((...-----(((((-((((....)))))))))..-..))))))))----...)..)))..)).))). ( -38.90)
>DroYak_CAF1 15499 111 + 1
UGAAGCCGUAGCAAAGGUUGGAGCCUUGGAGCCCACGGGCUCUGGAACAUUAAAUAAAUUUAAG-AACUGGGAGUGUUUUAAGG-GAAGAUUUAU----AAGCUGCCUGAACAGGUU
...(((((((((.(((((....)))))((((((....)))))).......(((((...(((.((-(((.......))))).)))-....))))).----..))))).......)))) ( -25.91)
>consensus
UGAAGCCGUAGCAAAGGUUGGAGCCUUGGAGCCCACGGGCUCUGAAAGUUCGAAUAAAUUUAGA_ACUUAGGAGUGUUUUGAGG_GACGAUUUAU____AAACUGCCUGAAUAGGUU
....(((.......(((..(.....(..(((((....)))))..).....................(((((((...)))))))...................)..))).....))). (-16.85 = -17.00 +   0.15)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,862,053 – 2,862,165
Length 112
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 72.96
Mean single sequence MFE -20.45
Consensus MFE -13.70
Energy contribution -12.82
Covariance contribution -0.89
Combinations/Pair 1.42
Mean z-score -1.02
Structure conservation index 0.67
SVM decision value 0.15
SVM RNA-class probability 0.606930
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2862053 112 - 20766785
AACCUAUUCAAGCAGUUA----AUUAAGCGAC-CCUCAAAACAAUCUUAAGUUUCCAAAUUUAUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCA
.........((((.((..----....(((((.-..............((((((....))))))...((.((((..(((((....))))).)))).))......))))))).)))).. ( -18.10)
>DroGri_CAF1 14303 110 - 1
UAAC-AUUCAGACAGUUAUCAAUUA--UAUAGUUUUCUAACGAAUUGUGACU--AUCUCU-CACU-CAAAUUCCAGAACCCGUCGGUGCCAAAGCGCCCACAUUUGCUAGUGUCUCA
....-....(((((.(((.(((...--....(..((((...(((((((((..--.....)-))).-..))))).))))..)((.(((((....))))).))..))).)))))))).. ( -20.80)
>DroSec_CAF1 13686 112 - 1
AACCUAUUCAGGCAGUUU----AAAAUUUGUC-CCUCAAAACACUCCUAAGUUUCCAAAUUUGUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCA
..(((.....((.(((((----.(((((((..-.....((((........)))).)))))))....))))).)).(((((....)))))..)))...........((....)).... ( -20.30)
>DroSim_CAF1 20381 112 - 1
AACCUAUUCAGGCAGUUU----AAUAAUCGUC-CCUCAAAACCAUCCUAAGUUUCAAAAUUGAUUUGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCU
..(((.....((.(((((----((..((((..-.....((((........))))......))))))))))).)).(((((....)))))..)))...........((....)).... ( -21.62)
>DroEre_CAF1 13280 106 - 1
CACCCACUCAGGCAGUUU----AACAAUCGUC-CCUCAAAACUCUCCUAAGU-CUUGA-----UUCCAACUUUCAGAGCCCGUGGGCUCCAAAGCUCCCACCUUUGCUACGGCUUCA
..........((.(((((----..........-..((((.(((......)))-.))))-----............(((((....)))))..))))).))......((....)).... ( -21.90)
>DroYak_CAF1 15499 111 - 1
AACCUGUUCAGGCAGCUU----AUAAAUCUUC-CCUUAAAACACUCCCAGUU-CUUAAAUUUAUUUAAUGUUCCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCA
..........((.(((((----..........-..(((((((.......)))-.)))).................(((((....)))))..))))))).......((....)).... ( -20.00)
>consensus
AACCUAUUCAGGCAGUUU____AAAAAUCGUC_CCUCAAAACAAUCCUAAGU_UCUAAAUUUAUUCGAACUUUCAGAGCCCGUGGGCUCCAAGGCUCCAACCUUUGCUACGGCUUCA
.........((((..............................................................(((((....)))))...(((..........)))...)))).. (-13.70 = -12.82 +  -0.89)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,862,133 – 2,862,234
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -32.14
Consensus MFE -16.55
Energy contribution -16.75
Covariance contribution 0.20
Combinations/Pair 1.28
Mean z-score -2.07
Structure conservation index 0.52
SVM decision value 0.46
SVM RNA-class probability 0.745862
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2862133 101 + 20766785
GAGGGUCGCUUAAU----UAACUGCUUGAAUAGGUUUGGGUUUAG-GUCAUGU-AGUACCUCAUAGCGGGAACUGGAUAGGCCUGAGCCUGACAAAGUAAAGCGAAA
.....((((((...----....(((((......(.(..(((((((-(((((.(-(((.(((......))).)))).)).))))))))))..)).))))))))))).. ( -33.51)
>DroSec_CAF1 13766 101 + 1
GAGGGACAAAUUUU----AAACUGCCUGAAUAGGUUUGGGUUUGG-GUAUUCU-AGUACCUCAUAGCGGGAACUGGAUAGGCCUGAGCCUGACAAAGUAGAGCAAAA
..............----....((((((.....(.(..((((..(-((..(((-(((.(((......))).))))))...)))..))))..))....))).)))... ( -31.60)
>DroSim_CAF1 20461 101 + 1
GAGGGACGAUUAUU----AAACUGCCUGAAUAGGUUUGGGUUUGG-GUCUUCU-AGUACCUCAUAGCGGGAACUGGAUAGGCCUGAGCCUGACAAAGUAGAGCAAAA
..............----....((((((.....(.(..((((..(-(((((((-(((.(((......))).)))))).)))))..))))..))....))).)))... ( -34.20)
>DroEre_CAF1 13354 101 + 1
GAGGGACGAUUGUU----AAACUGCCUGAGUGGGUGCGGGUUUAG-GUGUGUC-AGUACCUCAUGGCGGGAACUGGAUAGGCCUGAGCCUGACAAAGUAGAGCAAAG
.........(((((----..(((((((....)))).(((((((((-((.((((-(((.(((......))).))).)))).)))))))))))....)))..))))).. ( -36.80)
>DroYak_CAF1 15578 101 + 1
AAGGGAAGAUUUAU----AAGCUGCCUGAACAGGUUUGGGUUUUG-GUCUUAC-AGUACCUCAUGGCGGGAACUGGAUAGGCCUGUGCCUGACAGAGUAAAGCAAAG
..............----..(((((((....))))(..(((...(-((((..(-(((.(((......))).))))...)))))...)))..)........))).... ( -28.40)
>DroPer_CAF1 13794 103 + 1
AGGGUGCGGAUCUUCUAAAAACUGCCUGAAGAAG----GGUCUAGAGUGUUGGAUCUACCUCAUGAGUGGCACGGGAUAGGCCUGGGCCUGGCACAGCAAUGCGAAA
...((((((.(((((............))))).(----(((((((....)))))))).))........(((.((((.....)))).)))..))))............ ( -28.30)
>consensus
GAGGGACGAUUAUU____AAACUGCCUGAAUAGGUUUGGGUUUAG_GUCUUCU_AGUACCUCAUAGCGGGAACUGGAUAGGCCUGAGCCUGACAAAGUAAAGCAAAA
......................((((((.....((.(((((((((.((......(((.(((......))).)))......)))))))))))))....))).)))... (-16.55 = -16.75 +   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 09:41:23 2006