Locus 1117

Sequence ID 3R_DroMel_CAF1
Location 3,377,328 – 3,377,457
Length 129
Max. P 0.988246
window1828 window1829 window1830 window1831

overview

Window 8

Location 3,377,328 – 3,377,445
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.00
Mean single sequence MFE -36.28
Consensus MFE -20.55
Energy contribution -23.15
Covariance contribution 2.60
Combinations/Pair 1.09
Mean z-score -2.20
Structure conservation index 0.57
SVM decision value 1.08
SVM RNA-class probability 0.911639
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3377328 117 + 27905053
CC-CGGGGCUGAGAUUGGGUUAAGCAAGGGGAAGCCCCUAAAGAGCGAAGGUAAGGUAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGA--AAAGGUGCAAACCCAAAACUUAACUUUCC
..-.((((((....(((.......))).....))))))........((((((....(((((((..(((((((((((((.......))))--))).))))...))..))))))))))))). ( -37.90)
>DroSec_CAF1 5704 117 + 1
CC-AGGGGCUGAGAUUGGGUUAAGCAAGGGGAAGACCCCAAAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCCAGGGGA--AAAGGUGCAAACCCUAAACUUAACUUUCC
..-.((((((....(((.......))).....)).))))..........((.(((..(((((((.(((((((((((((.......))))--))).))))...)).)))))))..))).)) ( -36.90)
>DroAna_CAF1 14865 96 + 1
CCUAGGGCCUCAGAUUGGGUUAA------------------------AAGGUAAAAAGAGUUAAGAGUCACUUCUCCUGUUCAGGAGGAAAAAAGGUUCAAGCCAUAAAGUCAGCUUUUA
(((..(((((......)))))..------------------------.)))....(((((((.........(((((((....))))))).....(((....)))........))))))). ( -22.20)
>DroSim_CAF1 6542 116 + 1
CC-AGGGGCUGAGAUUGGGUUAAGCAAGG-GAAGCCCCCAAAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGA--AAAGGUGCAAACCCUAAACUUAACUUUCC
..-.((((((....(((.......)))..-..))))))...........((.(((..(((((((.(((((((((((((.......))))--))).))))...)).)))))))..))).)) ( -40.40)
>DroEre_CAF1 6210 117 + 1
CC-AGGGGCUGAGAUUGGGUUAAGCUAGGGGAAGCCCCUGAAGAGCGAAGGUGAGGGAAGUUUAAGGGCCCUUUUGCCGUUCACGGGGA--AAAGGUGCAAGCCAUAAACUUAACUUUCU
.(-(((((((....((((......))))....))))))))......((((((.....(((((((.((((((((((.((.......)).)--))))).))...)).))))))).)))))). ( -44.00)
>consensus
CC_AGGGGCUGAGAUUGGGUUAAGCAAGGGGAAGCCCCCAAAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGA__AAAGGUGCAAACCCUAAACUUAACUUUCC
....((((((......................))))))........((((((.....(((((((.(((((((((((((.......))))...)))))))...)).))))))).)))))). (-20.55 = -23.15 +   2.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,377,328 – 3,377,445
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.00
Mean single sequence MFE -33.21
Consensus MFE -17.61
Energy contribution -20.49
Covariance contribution 2.88
Combinations/Pair 1.16
Mean z-score -2.72
Structure conservation index 0.53
SVM decision value 2.11
SVM RNA-class probability 0.988246
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3377328 117 - 27905053
GGAAAGUUAAGUUUUGGGUUUGCACCUUU--UCCCCUUGAACGGGAAAAGUGCCCUUAAACUUACCUUACCUUCGCUCUUUAGGGGCUUCCCCUUGCUUAACCCAAUCUCAGCCCCG-GG
((.(((.(((((((.(((...((((.(((--((((.......)))))))))))))).))))))).))).))...........((((((.....(((.......)))....)))))).-.. ( -37.60)
>DroSec_CAF1 5704 117 - 1
GGAAAGUUAAGUUUAGGGUUUGCACCUUU--UCCCCUGGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUUUGGGGUCUUCCCCUUGCUUAACCCAAUCUCAGCCCCU-GG
((.(((..((((((((((...((((.(((--((((.......)))))))))))))))))))))..))).))...((.....((((....))))..))....................-.. ( -38.00)
>DroAna_CAF1 14865 96 - 1
UAAAAGCUGACUUUAUGGCUUGAACCUUUUUUCCUCCUGAACAGGAGAAGUGACUCUUAACUCUUUUUACCUU------------------------UUAACCCAAUCUGAGGCCCUAGG
.....(((.......(((.(((((.........(((((....))))).(((........)))..........)------------------------)))).)))......)))...... ( -13.82)
>DroSim_CAF1 6542 116 - 1
GGAAAGUUAAGUUUAGGGUUUGCACCUUU--UCCCCUUGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUUUGGGGGCUUC-CCUUGCUUAACCCAAUCUCAGCCCCU-GG
((.(((..((((((((((...((((.(((--((((.......)))))))))))))))))))))..))).))........(..((((((..-..(((.......)))....)))))).-.) ( -42.30)
>DroEre_CAF1 6210 117 - 1
AGAAAGUUAAGUUUAUGGCUUGCACCUUU--UCCCCGUGAACGGCAAAAGGGCCCUUAAACUUCCCUCACCUUCGCUCUUCAGGGGCUUCCCCUAGCUUAACCCAAUCUCAGCCCCU-GG
.(((((..(((((((.((...((.(((((--(..(((....))).)))))))))).)))))))..))....)))......((((((((......................)))))))-). ( -34.35)
>consensus
GGAAAGUUAAGUUUAGGGUUUGCACCUUU__UCCCCUUGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUUUAGGGGCUUCCCCUUGCUUAACCCAAUCUCAGCCCCU_GG
((.(((..((((((((((...((((.(((..((((.......)))))))))))))))))))))..))).))...........((((((......................)))))).... (-17.61 = -20.49 +   2.88)

alignment

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secondary structure

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Window 0

Location 3,377,367 – 3,377,457
Length 90
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 88.42
Mean single sequence MFE -31.60
Consensus MFE -22.80
Energy contribution -23.18
Covariance contribution 0.38
Combinations/Pair 1.08
Mean z-score -3.21
Structure conservation index 0.72
SVM decision value 1.34
SVM RNA-class probability 0.944335
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3377367 90 + 27905053
AAGAGCGAAGGUAAGGUAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGAAAAGGUGCAAACCCAAAACUUAACUUUCC---------UUCUUUU-GCGAG
....(((((((.((((.(((((.(((.(((((((((((.......))))))).))))..........)))))))).))---------)))))))-))... ( -32.00)
>DroSec_CAF1 5743 90 + 1
AAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCCAGGGGAAAAGGUGCAAACCCUAAACUUAACUUUCC---------UUCUUUU-GGGAG
......(((((.(((..(((((((.(((((((((((((.......))))))).))))...)).)))))))..))).))---------)))....-..... ( -33.70)
>DroSim_CAF1 6580 90 + 1
AAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGAAAAGGUGCAAACCCUAAACUUAACUUUCC---------UUCUUUU-GGGAG
......(((((.(((..(((((((.(((((((((((((.......))))))).))))...)).)))))))..))).))---------)))....-..... ( -33.70)
>DroEre_CAF1 6249 100 + 1
AAGAGCGAAGGUGAGGGAAGUUUAAGGGCCCUUUUGCCGUUCACGGGGAAAAGGUGCAAGCCAUAAACUUAACUUUCUCUGGAUACAUUCUUUUCGGCAG
....((((((((.....(((((((.((((((((((.((.......)).)))))).))...)).))))))).))))))...(((.....))).....)).. ( -27.00)
>consensus
AAGAGCGAAGGUAAGGGAAGUUUAAGGGCACUUUUCCCGUUCAAGGGGAAAAGGUGCAAACCCUAAACUUAACUUUCC_________UUCUUUU_GGGAG
.........((.(((..(((((((.(((((((((((((.......))))))).))))...)).)))))))..))).))...................... (-22.80 = -23.18 +   0.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,377,367 – 3,377,457
Length 90
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 88.42
Mean single sequence MFE -31.42
Consensus MFE -22.62
Energy contribution -24.12
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -4.73
Structure conservation index 0.72
SVM decision value 1.15
SVM RNA-class probability 0.923356
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3377367 90 - 27905053
CUCGC-AAAAGAA---------GGAAAGUUAAGUUUUGGGUUUGCACCUUUUCCCCUUGAACGGGAAAAGUGCCCUUAAACUUACCUUACCUUCGCUCUU
.....-....(((---------((.(((.(((((((.(((...((((.(((((((.......)))))))))))))).))))))).))).)))))...... ( -32.90)
>DroSec_CAF1 5743 90 - 1
CUCCC-AAAAGAA---------GGAAAGUUAAGUUUAGGGUUUGCACCUUUUCCCCUGGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUU
.....-....(((---------((.(((..((((((((((...((((.(((((((.......)))))))))))))))))))))..))).)))))...... ( -35.70)
>DroSim_CAF1 6580 90 - 1
CUCCC-AAAAGAA---------GGAAAGUUAAGUUUAGGGUUUGCACCUUUUCCCCUUGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUU
.....-....(((---------((.(((..((((((((((...((((.(((((((.......)))))))))))))))))))))..))).)))))...... ( -35.70)
>DroEre_CAF1 6249 100 - 1
CUGCCGAAAAGAAUGUAUCCAGAGAAAGUUAAGUUUAUGGCUUGCACCUUUUCCCCGUGAACGGCAAAAGGGCCCUUAAACUUCCCUCACCUUCGCUCUU
....................((((..((..(((((((.((...((.((((((..(((....))).)))))))))).)))))))..))........)))). ( -21.40)
>consensus
CUCCC_AAAAGAA_________GGAAAGUUAAGUUUAGGGUUUGCACCUUUUCCCCUUGAACGGGAAAAGUGCCCUUAAACUUCCCUUACCUUCGCUCUU
......................((.(((..((((((((((...((((.(((((((.......)))))))))))))))))))))..))).))......... (-22.62 = -24.12 +   1.50)

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 10:01:22 2006