Locus 6169

Sequence ID 3R_DroMel_CAF1
Location 16,161,136 – 16,161,303
Length 167
Max. P 0.999915
window10054 window10055 window10056 window10057

overview

Window 4

Location 16,161,136 – 16,161,246
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 89.92
Mean single sequence MFE -19.08
Consensus MFE -14.32
Energy contribution -15.52
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.75
SVM decision value 0.67
SVM RNA-class probability 0.817162
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16161136 110 - 27905053
ACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACACUCUCGAACAAAAAAAAAAAAGCUUGUGAAACUAAAAUAGAAACACAUUUCAU
........((((((((((((.......)))))))((((....))))..............)))))................((((...(((...)))...))))...... ( -18.30)
>DroSec_CAF1 30714 108 - 1
ACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACUC-CUCGAACAAAAAA-AUAAAGCUUGUGAAACUAAAAUAGAAACACAUUUCAU
........((((((((((((.......)))))))((((....))))............-.))))).......-........((((...(((...)))...))))...... ( -18.30)
>DroSim_CAF1 32881 106 - 1
ACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACA--CACACUC-CUCGAACAAAAAA-AUAAAGCUUGUGAAACUAAAAUAGAAACACAUUUCAU
........((((((((((((.......)))))))((((....))))...--.......-.))))).......-........((((...(((...)))...))))...... ( -18.30)
>DroEre_CAF1 30681 109 - 1
ACCUCUACUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACACACUCGAACAAAAAA-AUAAAGCUUGUGAAACUAAAAUAGAAACACAUUUCAU
........((((((((((((.......)))))))((((....))))..............))))).......-........((((...(((...)))...))))...... ( -18.30)
>DroAna_CAF1 27046 94 - 1
ACCUCGUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACAUACG---------------AAAAAA-AUAGGGCUUGGGAAACUAAAAUAGAAACACAUUUCAU
.(((....((((.(((((((.......)))))))((((....))))...))---------------))....-..)))..((((....))))....((((....)))).. ( -22.20)
>consensus
ACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACAC_CUCGAACAAAAAA_AUAAAGCUUGUGAAACUAAAAUAGAAACACAUUUCAU
........((((((((((((.......)))))))((((....))))..............)))))................((((...(((...)))...))))...... (-14.32 = -15.52 +   1.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,161,176 – 16,161,274
Length 98
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 82.04
Mean single sequence MFE -32.46
Consensus MFE -17.68
Energy contribution -20.80
Covariance contribution 3.12
Combinations/Pair 1.10
Mean z-score -4.23
Structure conservation index 0.54
SVM decision value 2.82
SVM RNA-class probability 0.997246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16161176 98 + 27905053
UUUUGUUCGAGAGUGUGUGUGUGUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUCGGCAAA-UACAAAAUAACAAAAAAGG
(((((((...(((((((((.(((....))).)))))))))..(((((((((.....(((......))).....))))))-))).....))))))).... ( -36.60)
>DroSec_CAF1 30753 97 + 1
UUUUGUUCGAG-GAGUGUGUGUGUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA-UACAAAAUUGCAAAAAAUG
(((((((((((-..(((((.(((....))).))))).)))))(((((((((.....(((......))).....))))))-)))......)))))).... ( -35.40)
>DroSim_CAF1 32920 95 + 1
UUUUGUUCGAG-GAGUGUG--UGUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA-UACAAAAUAGCAAAAAAUG
(((((((....-(((((((--((........)))))))))..(((((((((.....(((......))).....))))))-))).....))))))).... ( -34.20)
>DroEre_CAF1 30720 96 + 1
UUUUGUUCGAGUGUGUGUGUGUGUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGUAGAGGUUUUGGCAAA-UACAAAAUAACAAAAAA--
(((((((((((((((((.((((....)))).)))))))))))(((((((((.....(((......))).....))))))-)))......))))))..-- ( -40.90)
>DroAna_CAF1 27085 83 + 1
UUUU---------------CGUAUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGACGAGGUUCGGUUUGCUUUCUCUCCACCAAAAAAA-
..((---------------((..((((......))))..)))).((..(((.....((((....))))....)))..))...................- ( -15.20)
>consensus
UUUUGUUCGAG_GAGUGUGUGUGUGUGCAUUUACACGCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA_UACAAAAUAACAAAAAAUG
(((((((((((...(((((.(((....))).))))).)))))(((((((((.....(((......))).....)))))).)))......)))))).... (-17.68 = -20.80 +   3.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,161,176 – 16,161,274
Length 98
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 82.04
Mean single sequence MFE -22.28
Consensus MFE -13.48
Energy contribution -14.48
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.73
Structure conservation index 0.60
SVM decision value 1.56
SVM RNA-class probability 0.963599
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16161176 98 - 27905053
CCUUUUUUGUUAUUUUGUA-UUUGCCGAAACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACACUCUCGAACAAAA
....(((((((.....((.-((((((..((.(((......))).))..)))))).)).((((.((((...((......))...)))).))))))))))) ( -25.20)
>DroSec_CAF1 30753 97 - 1
CAUUUUUUGCAAUUUUGUA-UUUGCCAAAACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACUC-CUCGAACAAAA
............((((((.-((((((..((.(((......))).))..))))))...(((((.((((...((....))...))))..-))))))))))) ( -21.40)
>DroSim_CAF1 32920 95 - 1
CAUUUUUUGCUAUUUUGUA-UUUGCCAAAACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACA--CACACUC-CUCGAACAAAA
............((((((.-((((((..((.(((......))).))..))))))...(((((.((((...........--.))))..-))))))))))) ( -20.80)
>DroEre_CAF1 30720 96 - 1
--UUUUUUGUUAUUUUGUA-UUUGCCAAAACCUCUACUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACACACUCGAACAAAA
--..(((((((.....((.-((((((..((.(((......))).))..)))))).)).((((.((((...((......))...)))).))))))))))) ( -24.60)
>DroAna_CAF1 27085 83 - 1
-UUUUUUUGGUGGAGAGAAAGCAAACCGAACCUCGUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACAUACG---------------AAAA
-....((((((.............)))))).......((((.(((((((.......)))))))((((....))))...))---------------)).. ( -19.42)
>consensus
CAUUUUUUGCUAUUUUGUA_UUUGCCAAAACCUCUUCUUCGAGUUUGAGGCAAACACUCGAGCGUGUAAAUGCACACACACACACAC_CUCGAACAAAA
.....................................((((((((((((.......)))))))((((....))))..............)))))..... (-13.48 = -14.48 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,161,212 – 16,161,303
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 73.54
Mean single sequence MFE -17.54
Consensus MFE -9.96
Energy contribution -10.44
Covariance contribution 0.48
Combinations/Pair 1.17
Mean z-score -3.56
Structure conservation index 0.57
SVM decision value 4.53
SVM RNA-class probability 0.999915
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16161212 91 + 27905053
GCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUCGGCAAA-UACAAAAUAACAAAAAAGGUGAAAUAAACCAAAAAAAAAAAAAAUUCA
....(((((((((((.....(((......))).....))))))-)))..............(((.......)))...............)). ( -20.20)
>DroSec_CAF1 30788 86 + 1
GCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA-UACAAAAUUGCAAAAAAUG--A---AAAUGAAAAACCAAAAAAUUGAA
..(((((((((((((.....(((......))).....))))))-)))....(((......((.--.---..)).......)))....)))). ( -18.32)
>DroSim_CAF1 32953 86 + 1
GCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA-UACAAAAUAGCAAAAAAUG--A---AAAUGAAAAACCAAAAAAUUGAA
(((...(((((((((.....(((......))).....))))))-))).....)))........--.---....................... ( -19.00)
>DroEre_CAF1 30756 71 + 1
GCUCGAGUGUUUGCCUCAAACUCGAAGUAGAGGUUUUGGCAAA-UACAAAAUAACAAAAAA--------------------AAAAAAACUAA
......(((((((((.....(((......))).....))))))-)))..............--------------------........... ( -17.70)
>DroAna_CAF1 27106 82 + 1
GCUCGAGUGUUUGCCUCAAACUCGAAGACGAGGUUCGGUUUGCUUUCUCUCCACCAAAAAAA-----AAAAACCAAAAAUA-----AUAAAA
....(((.((..(((.....((((....))))....)))..))...))).............-----..............-----...... ( -12.50)
>consensus
GCUCGAGUGUUUGCCUCAAACUCGAAGAAGAGGUUUUGGCAAA_UACAAAAUAACAAAAAAUG__A___AAACCAAAAACAAAAAAAUUGAA
......(((((((((.....(((......))).....)))))).)))............................................. ( -9.96 = -10.44 +   0.48)

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 12:14:27 2006