Locus 7070

Sequence ID 2L_DroMel_CAF1
Location 19,798,844 – 19,799,029
Length 185
Max. P 0.969754
window11272 window11273 window11274

overview

Window 2

Location 19,798,844 – 19,798,953
Length 109
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 86.18
Mean single sequence MFE -25.04
Consensus MFE -17.63
Energy contribution -18.63
Covariance contribution 1.00
Combinations/Pair 1.25
Mean z-score -3.58
Structure conservation index 0.70
SVM decision value 0.55
SVM RNA-class probability 0.777084
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19798844 109 - 22407834
AUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCAAAAU-----UCGAAAAAGGCCAAAAACGAGCUGAAAUUCAAAUAGAAAAGAAAACACUCGAAAUUGAAGUGCUG
.....(((((....((((((((.......))))))))((((..(-----((((....((((......).)))....(((.....)))..........))))).)))).))))). ( -27.50)
>DroSec_CAF1 65409 108 - 1
AUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUGAAAAU-----UCGAAAAAGGCCAA-AACGAGCUGAAAUUCAAACAGAAAAGAAAACACUCGAAAUUGAAGUGCUG
.....(((((...(((((((((.......))))))))).....(-----((((....(((...-.....)))....(((.....)))..........)))))......))))). ( -27.40)
>DroSim_CAF1 66652 108 - 1
AUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUAAAAAU-----UCGAAAAAGGCCAA-AACGAGCUGAAAUUCAAAUAGAAAAGAAAACACUCGAAAUUGAAGUGCUG
.....(((((...(((((((((.......))))))))).....(-----((((....(((...-.....)))....(((.....)))..........)))))......))))). ( -27.40)
>DroEre_CAF1 66807 108 - 1
AUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGUUCAAAAU-----UCGAAAAAGGCCAA-AACAAGCUGAAAUUCAAAUAGAAAAGAAAACACUCGAAAUUGAAGUGCUG
.....(((((....((((((((.......))))))))((((..(-----((((....(((...-.....)))....(((.....)))..........))))).)))).))))). ( -25.30)
>DroYak_CAF1 67775 108 - 1
AUAAAAGUACAAAGGCCCCAAACUCGCAUUUUGGGGUUCAAAAU-----UCAAAAAAGGCCAA-AACGAGCUAAAAUUCAAAUAGAAAAAAAAACACUGGAAAUUGAAGUGCUG
.....(((((....((((((((.......))))))))((((..(-----(((.....(((...-.....)))....(((.....)))..........))))..)))).))))). ( -21.20)
>DroAna_CAF1 64586 106 - 1
GAAAAAGAGCAAAA--CCCAACCUCACAA-----AGUUUACAUUUCAGGUUGGAAAAGGCAGA-AAGGAGCCAAAAUUCGGAUAGAAAAGAAAGCACUCUAAAUUGAAGUGCUG
(((...........--.(((((((.....-----............)))))))....(((...-.....)))....))).............(((((((......).)))))). ( -21.43)
>consensus
AUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCAAAAU_____UCGAAAAAGGCCAA_AACGAGCUGAAAUUCAAAUAGAAAAGAAAACACUCGAAAUUGAAGUGCUG
.....(((((...(((((((((.......)))))))))...........((((....(((.........)))....(((.....)))..........)))).......))))). (-17.63 = -18.63 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,798,879 – 19,798,993
Length 114
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 80.70
Mean single sequence MFE -22.14
Consensus MFE -13.49
Energy contribution -15.10
Covariance contribution 1.61
Combinations/Pair 1.24
Mean z-score -2.31
Structure conservation index 0.61
SVM decision value 0.77
SVM RNA-class probability 0.847248
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19798879 114 - 22407834
CAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCAAAAU-----UCGAAAAAGGCCAAAAACGAGCUGAAAUUC
..(((((.......)))))........(((..((............)).....(((((((((.......)))))))))......-----....................)))....... ( -23.50)
>DroSec_CAF1 65444 111 - 1
CAGGUGUACA--UAGCACCAAUAAUAGGGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUGAAAAU-----UCGAAAAAGGCCAA-AACGAGCUGAAAUUC
..(((((...--..)))))........(((..((............)).....(((((((((.......)))))))))......-----.........)))..-............... ( -26.60)
>DroSim_CAF1 66687 113 - 1
CAGGUGUACAAGUAGCACCAAUAACAAGGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUAAAAAU-----UCGAAAAAGGCCAA-AACGAGCUGAAAUUC
..(((((.......)))))........(((..((............)).....(((((((((.......)))))))))......-----.........)))..-............... ( -26.50)
>DroEre_CAF1 66842 113 - 1
CAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGUUCAAAAU-----UCGAAAAAGGCCAA-AACAAGCUGAAAUUC
..(((((.......)))))........(((..((............)).....((((......(((.((((((.....))))))-----.)))....))))..-.....)))....... ( -22.90)
>DroYak_CAF1 67810 113 - 1
CAGGUGUACAAAUAGCGCCAAUAAUAAAGCAAGCAUAACCAUAAAAGUACAAAGGCCCCAAACUCGCAUUUUGGGGUUCAAAAU-----UCAAAAAAGGCCAA-AACGAGCUAAAAUUC
..(((((.......)))))............(((...................(((((((((.......)))))))))......-----........(.....-..)..)))....... ( -18.90)
>DroAna_CAF1 64621 99 - 1
CAGAUGUUUAAA------------GAAAACAAACAAAAUUGAAAAAGAGCAAAA--CCCAACCUCACAA-----AGUUUACAUUUCAGGUUGGAAAAGGCAGA-AAGGAGCCAAAAUUC
....(((((...------------..))))).......................--.(((((((.....-----............)))))))....(((...-.....)))....... ( -14.43)
>consensus
CAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCAAAAU_____UCGAAAAAGGCCAA_AACGAGCUGAAAUUC
..(((((.......)))))..................................(((((((((.......)))))))))...................(((.........)))....... (-13.49 = -15.10 +   1.61)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,798,913 – 19,799,029
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.04
Mean single sequence MFE -24.87
Consensus MFE -12.23
Energy contribution -13.98
Covariance contribution 1.75
Combinations/Pair 1.21
Mean z-score -2.37
Structure conservation index 0.49
SVM decision value 1.65
SVM RNA-class probability 0.969754
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19798913 116 - 22407834
AGCUAAAUG-ACCUAAAAACUGGAAAGG---GUAUCGAAACAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCA
.(((.....-.((........))....(---((.........(((((.......))))).........(....)...))).....))).....(((((((((.......))))))))).. ( -26.50)
>DroSec_CAF1 65477 114 - 1
AGCUAAAGG-UCCUAAAAAUUCGAAAGG---GUAUUGAAACAGGUGUACA--UAGCACCAAUAAUAGGGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUGA
.(((....(-(((((...((((....))---)).........(((((...--..))))).....)))))).)))...................(((((((((.......))))))))).. ( -35.70)
>DroSim_CAF1 66720 116 - 1
AGCUAGAGG-ACCUGAAAAUUCGAAAGG---GUAUUGAAACAGGUGUACAAGUAGCACCAAUAACAAGGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUAA
.(((....(-.(((....((((....))---)).........(((((.......))))).......)))).)))...................(((((((((.......))))))))).. ( -29.60)
>DroEre_CAF1 66875 115 - 1
AACUAAAUG-ACC-AGAGUGUCCAGAGA---GUAUCGAAACAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGUUCA
.........-...-...((((...((..---...))......(((((.......)))))...........................))))...(((((((((.......))))))))).. ( -21.40)
>DroYak_CAF1 67843 116 - 1
AACUAAAUGGACC-AGAGUGUCCAGAGA---GUAUCGAAACAGGUGUACAAAUAGCGCCAAUAAUAAAGCAAGCAUAACCAUAAAAGUACAAAGGCCCCAAACUCGCAUUUUGGGGUUCA
.(((...(((((.-.....)))))...)---)).........(((((.......)))))..................................(((((((((.......))))))))).. ( -26.20)
>DroAna_CAF1 64659 100 - 1
AGUUUUAAG-GAAGAAAACCUUCAAAGGACAAUAUCAUACCAGAUGUUUAAA------------GAAAACAAACAAAAUUGAAAAAGAGCAAAA--CCCAACCUCACAA-----AGUUUA
.(((((...-((((.....))))..)))))((((((......))))))....------------......((((....((....))(((.....--......)))....-----.)))). (  -9.80)
>consensus
AGCUAAAUG_ACCUAAAAACUCCAAAGG___GUAUCGAAACAGGUGUACAAAUAGCACCAAUAAUAAAGCAAGCAUAACCAUAAAAGCACAAAGGCCCCAAACUCGCAUUUUGGGGCUCA
..........................................(((((.......)))))..................................(((((((((.......))))))))).. (-12.23 = -13.98 +   1.75)

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 12:26:34 2006