Locus 3735

Sequence ID X_DroMel_CAF1
Location 9,948,678 – 9,948,835
Length 157
Max. P 0.938508
window6123 window6124 window6125 window6126

overview

Window 3

Location 9,948,678 – 9,948,795
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.79
Mean single sequence MFE -36.13
Consensus MFE -24.77
Energy contribution -25.90
Covariance contribution 1.13
Combinations/Pair 1.06
Mean z-score -2.68
Structure conservation index 0.69
SVM decision value 1.27
SVM RNA-class probability 0.938508
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9948678 117 + 22224390
CAAGGCACUCGGCUAUGCCAUU---UCUUUUGUGUUUUUUAAUAAACAAUUAAAAAACCAUUUGGCAGCGCGACAUGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGA
...(((.....))).((((...---........((((((((((.....))))))))))((((((..((((((....(((.((((....)))))))..)))).))..))))))..)))).. ( -38.40)
>DroSec_CAF1 11563 117 + 1
CAAGGCGUUCGGCUAUGCCAAU---UCUUUUGUGUUUUUUAAUAAACAAUUAAAAAACCAUUUGGCACCGUGACAUGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGA
....((.(((((...((((((.---.....((.((((((((((.....)))))))))))).))))))))((((((((((.((((....)))))))...)))..))))....))).))... ( -38.00)
>DroEre_CAF1 11412 117 + 1
CAAGGCACUCUGCAAAUCUGUU---UUUGUUUUGUUUUUUAAUAAACAAUUAAAAACCCAUUUGGCUGCGGGACAAGAGAGGGGAAUCCCCCCGCCACGUGACUCACAAAUGAAGGCAGA
........(((((......(((---((((..((((((......)))))).))))))).(((((((..(((((......(.((((....))))).)).)))..)...))))))...))))) ( -29.50)
>DroYak_CAF1 11094 118 + 1
CAUGGCACUCGGCAAAGCUGUUGCCUUUGGUU--UUUUUUAACAAACAAUUAAAAAACCAUUUGGCUGCGCGAACAGCGAGGGGAUUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGA
.........((((...))))((((((((((((--((((.............))))))))(((((...(((((...((((.((((....)))))))).)))).)...))))))))))))). ( -38.62)
>consensus
CAAGGCACUCGGCAAAGCCAUU___UCUGUUGUGUUUUUUAAUAAACAAUUAAAAAACCAUUUGGCAGCGCGACAAGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGA
....((.....))...(((..............((((((((((.....))))))))))((((((....((((....(((.((((....)))))))..)))).....))))))..)))... (-24.77 = -25.90 +   1.13)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,948,678 – 9,948,795
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.79
Mean single sequence MFE -36.40
Consensus MFE -25.27
Energy contribution -26.40
Covariance contribution 1.13
Combinations/Pair 1.09
Mean z-score -2.08
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.825308
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9948678 117 - 22224390
UCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCGCGCUGCCAAAUGGUUUUUUAAUUGUUUAUUAAAAAACACAAAAGA---AAUGGCAUAGCCGAGUGCCUUG
(((.....((((((..((((((((.((((((((...)))))))))))).).)))..))))))((((((((((.....)))))))))).....)))---...(((((......)))))... ( -39.30)
>DroSec_CAF1 11563 117 - 1
UCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCACGGUGCCAAAUGGUUUUUUAAUUGUUUAUUAAAAAACACAAAAGA---AUUGGCAUAGCCGAACGCCUUG
...((.(((........((.((((.((((((((...)))))))))))).)).(((((((.((((((((((((.....)))))))))).)).....---.)))))))....))).)).... ( -37.60)
>DroEre_CAF1 11412 117 - 1
UCUGCCUUCAUUUGUGAGUCACGUGGCGGGGGGAUUCCCCUCUCUUGUCCCGCAGCCAAAUGGGUUUUUAAUUGUUUAUUAAAAAACAAAACAAA---AACAGAUUUGCAGAGUGCCUUG
...((.....((((..((((...((((.(.(((((...........))))).).)))).....((((((..((((((......))))))...)))---))).))))..))))..)).... ( -31.60)
>DroYak_CAF1 11094 118 - 1
UCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAAUCCCCUCGCUGUUCGCGCAGCCAAAUGGUUUUUUAAUUGUUUGUUAAAAAA--AACCAAAGGCAACAGCUUUGCCGAGUGCCAUG
.............(((.(.(((.((((((((((...)))))))))).(((.((.......((((((((((((.....))))..)))--)))))(((((....))))))))))))))))). ( -37.10)
>consensus
UCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCGCGCAGCCAAAUGGUUUUUUAAUUGUUUAUUAAAAAACAAAAAAAA___AACAGCAUAGCCGAGUGCCUUG
((.((...((((((...((..((((((((((((...)))))))))....)))..))))))))((((((((((.....))))))))))....................)).))........ (-25.27 = -26.40 +   1.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,948,715 – 9,948,835
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -24.58
Consensus MFE -19.62
Energy contribution -20.00
Covariance contribution 0.38
Combinations/Pair 1.04
Mean z-score -2.38
Structure conservation index 0.80
SVM decision value 0.75
SVM RNA-class probability 0.841568
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9948715 120 + 22224390
AAUAAACAAUUAAAAAACCAUUUGGCAGCGCGACAUGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGAAAACUGAAGCUAAAAAUAAUUAUAAAAUGUUCAGCAAAAA
....((((..........((((((..((((((....(((.((((....)))))))..)))).))..))))))....(((....))).....................))))......... ( -26.30)
>DroSec_CAF1 11600 120 + 1
AAUAAACAAUUAAAAAACCAUUUGGCACCGUGACAUGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGAAAACUGAAGCUAAAAAUAAUUAUAAGAUGUUCAGCAAAAA
....................((((((.((((.((..(((.((((....)))))))...)).))(((....))).))(((....)))..)))))).......................... ( -23.90)
>DroEre_CAF1 11449 120 + 1
AAUAAACAAUUAAAAACCCAUUUGGCUGCGGGACAAGAGAGGGGAAUCCCCCCGCCACGUGACUCACAAAUGAAGGCAGAAAACUGAAGCUAAAAAUAAUUAUAAGAUAUUCAGCAAAAA
....................(((((((.(((.........((((.....))))(((.(((.........)))..)))......))).))))))).......................... ( -22.50)
>DroYak_CAF1 11132 120 + 1
AACAAACAAUUAAAAAACCAUUUGGCUGCGCGAACAGCGAGGGGAUUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGAAAACCGAAGCUAAAAAUAAUUAUAAGAUAUUCAGCAAAAA
.......(((((......((((((...(((((...((((.((((....)))))))).)))).)...))))))..(((...........))).....)))))................... ( -25.60)
>consensus
AAUAAACAAUUAAAAAACCAUUUGGCAGCGCGACAAGCGAGGGGAAUCCCCCCGCUACGUGACUCACAAAUGAAGGCAGAAAACUGAAGCUAAAAAUAAUUAUAAGAUAUUCAGCAAAAA
.......(((((......((((((....((((....(((.((((....)))))))..)))).....))))))..(((...........))).....)))))................... (-19.62 = -20.00 +   0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,948,715 – 9,948,835
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -30.15
Consensus MFE -23.85
Energy contribution -24.47
Covariance contribution 0.62
Combinations/Pair 1.09
Mean z-score -2.41
Structure conservation index 0.79
SVM decision value 0.69
SVM RNA-class probability 0.824056
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9948715 120 - 22224390
UUUUUGCUGAACAUUUUAUAAUUAUUUUUAGCUUCAGUUUUCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCGCGCUGCCAAAUGGUUUUUUAAUUGUUUAUU
.......((((((.((...((((((((.((((..(((....))).............((.((((.((((((((...)))))))))))).))))))..))))))))....)).)))))).. ( -31.30)
>DroSec_CAF1 11600 120 - 1
UUUUUGCUGAACAUCUUAUAAUUAUUUUUAGCUUCAGUUUUCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCACGGUGCCAAAUGGUUUUUUAAUUGUUUAUU
.....((((((...............))))))..(((((........(((((((.(.((.((((.((((((((...)))))))))))).))....))))))))......)))))...... ( -29.40)
>DroEre_CAF1 11449 120 - 1
UUUUUGCUGAAUAUCUUAUAAUUAUUUUUAGCUUCAGUUUUCUGCCUUCAUUUGUGAGUCACGUGGCGGGGGGAUUCCCCUCUCUUGUCCCGCAGCCAAAUGGGUUUUUAAUUGUUUAUU
.....((((((...............))))))..(((((....(((((((....)))).((..((((.(.(((((...........))))).).))))..)))))....)))))...... ( -27.06)
>DroYak_CAF1 11132 120 - 1
UUUUUGCUGAAUAUCUUAUAAUUAUUUUUAGCUUCGGUUUUCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAAUCCCCUCGCUGUUCGCGCAGCCAAAUGGUUUUUUAAUUGUUUGUU
...(((((((((..(((((((........(((....)))............)))))))......(((((((((...)))))))))))))).)))).((((..(((....)))..)))).. ( -32.85)
>consensus
UUUUUGCUGAACAUCUUAUAAUUAUUUUUAGCUUCAGUUUUCUGCCUUCAUUUGUGAGUCACGUAGCGGGGGGAUUCCCCUCGCAUGUCGCGCAGCCAAAUGGUUUUUUAAUUGUUUAUU
.....((((((...............))))))..(((((........(((((((...((..((((((((((((...)))))))))....)))..)))))))))......)))))...... (-23.85 = -24.47 +   0.62)

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 11:06:58 2006