Locus 3740

Sequence ID X_DroMel_CAF1
Location 9,954,459 – 9,954,688
Length 229
Max. P 0.889551
window6137 window6138 window6139 window6140

overview

Window 7

Location 9,954,459 – 9,954,579
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.78
Mean single sequence MFE -22.17
Consensus MFE -16.20
Energy contribution -16.45
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.73
SVM decision value 0.58
SVM RNA-class probability 0.790339
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9954459 120 + 22224390
UUUUUUGCUUUUGCUUGUUCUUUGCUUCGUUGCUUUGUUUUAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCUUUUGCCUCAAAGGCAAAGCCCA
..(((((((((((..........((.((((((...(((((((((((.....))(((....))).)))))))))....)))))).))...(((........)))..))))))))))).... ( -24.50)
>DroSec_CAF1 17005 112 + 1
UUUUUUUGC----CUUGUUCUUUGCUUCGUUGCUUUGUUUUAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGCAAAGC---
...((((((----(((.......((.((((((...(((((((((((.....))(((....))).)))))))))....)))))).))...(((......-.)))....))))))))).--- ( -23.90)
>DroEre_CAF1 17091 106 + 1
UUCU---CC----CUUGUUCU------CUUUGCAUUGUUUUAAUGGCUUUUCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGAAAAGCCUA
....---..----........------.................(((((((((.((((((((.(((........)))))))))))....(((......-.)))......))))))))).. ( -21.90)
>DroYak_CAF1 16875 104 + 1
UUUU---CC----CUUGUUC--------UUUGCUUUGUUUUAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGAAAAGCCUA
....---..----.......--------................((((((....((((((((.(((........))))))))))).........((((-(((...))))))))))))).. ( -18.40)
>consensus
UUUU___CC____CUUGUUCU______CGUUGCUUUGUUUUAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU_UUGCCUCAAAGGAAAAGCCUA
............................................((((((.((.((((((((.(((........)))))))))))....(((........)))......)).)))))).. (-16.20 = -16.45 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,954,459 – 9,954,579
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -20.55
Consensus MFE -15.76
Energy contribution -16.45
Covariance contribution 0.69
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.77
SVM decision value 0.17
SVM RNA-class probability 0.616543
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9954459 120 - 22224390
UGGGCUUUGCCUUUGAGGCAAAAGGAUAUGCAAAGCACCGUUAAACGUAUUUUAAUUACAACAAUGUGGGAAAGCCAUUAAAACAAAGCAACGAAGCAAAGAACAAGCAAAAGCAAAAAA
((..((((((.((((..((....((...(((...)))))(((....(((.......)))......((((.....))))...)))...))..))))))))))..)).((....))...... ( -22.90)
>DroSec_CAF1 17005 112 - 1
---GCUUUGCCUUUGAGGCAA-AGGAUAUGCAAAGCACCGUUAAACGUAUUUUAAUUACAACAAUGUGGGAAAGCCAUUAAAACAAAGCAACGAAGCAAAGAACAAG----GCAAAAAAA
---((((((((((((...)))-))).........((..((((....(((.......)))......((((.....))))...........))))..))......))))----))....... ( -20.70)
>DroEre_CAF1 17091 106 - 1
UAGGCUUUUCCUUUGAGGCAA-AGGAUAUGCAAAGCACCGUUAAACGUAUUUUAAUUACAACAAUGUGGAAAAGCCAUUAAAACAAUGCAAAG------AGAACAAG----GG---AGAA
......(((((((((..(((.-......)))...(((..(((....(((.......)))......((((.....))))...)))..)))....------....))))----))---))). ( -19.70)
>DroYak_CAF1 16875 104 - 1
UAGGCUUUUCCUUUGAGGCAA-AGGAUAUGCAAAGCACCGUUAAACGUAUUUUAAUUACAACAAUGUGGGAAAGCCAUUAAAACAAAGCAAA--------GAACAAG----GG---AAAA
..(((((((((.(((..(((.-......)))...............(((.......)))..)))...)))))))))................--------.......----..---.... ( -18.90)
>consensus
UAGGCUUUGCCUUUGAGGCAA_AGGAUAUGCAAAGCACCGUUAAACGUAUUUUAAUUACAACAAUGUGGGAAAGCCAUUAAAACAAAGCAAAG______AGAACAAG____GG___AAAA
..(((((((((.(((..(((........)))...............(((.......)))..)))...)))))))))............................................ (-15.76 = -16.45 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,954,499 – 9,954,619
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.40
Mean single sequence MFE -29.12
Consensus MFE -24.92
Energy contribution -25.05
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -1.64
Structure conservation index 0.86
SVM decision value 0.03
SVM RNA-class probability 0.550726
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9954499 120 + 22224390
UAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCUUUUGCCUCAAAGGCAAAGCCCACGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAA
...(((.....)))((((((((.(((........)))))))))))...(((......(((((((.....)))))))((((......))))))).(((((((((........))))))))) ( -29.30)
>DroSec_CAF1 17041 113 + 1
UAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGCAAAGC------ACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAA
.....((...((((....((((.(((........)))))))((((((((((.....((-(((...))))))))))))------)))))))))..(((((((((........))))))))) ( -30.20)
>DroEre_CAF1 17118 119 + 1
UAAUGGCUUUUCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGAAAAGCCUACGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAA
....(((((((((.((((((((.(((........)))))))))))....(((......-.)))......)))))))))................(((((((((........))))))))) ( -30.40)
>DroYak_CAF1 16900 119 + 1
UAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU-UUGCCUCAAAGGAAAAGCCUACGAACUUGGGGCAUUUUCUCAAGAGUUUUUCUUUGGGAAA
........((((((.....(((((.........((.....))..(((((.....((((-(((...)))))))))))).))))).(((((((.....)))))))..........)))))). ( -26.60)
>consensus
UAAUGGCUUUCCCACAUUGUUGUAAUUAAAAUACGUUUAACGGUGCUUUGCAUAUCCU_UUGCCUCAAAGGAAAAGCCUACGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAA
........(((((.((((((((.(((........)))))))))))....(((........)))....((((((((((.......(((((((.....))))))).))))))))))))))). (-24.92 = -25.05 +   0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,954,579 – 9,954,688
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 94.65
Mean single sequence MFE -26.90
Consensus MFE -24.17
Energy contribution -23.80
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.90
SVM decision value 0.96
SVM RNA-class probability 0.889551
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9954579 109 + 22224390
CGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAACGAACAACAAAGUUGAAAAUUACCUUCUCGUACAGUGAAAACCAUUCAUGUGUGUCUCGAGUAUUUUAU
...((((((((((((((((((((........)))))))))....((((...))))................(((.((((.....))))))))))))))))))....... ( -25.60)
>DroSec_CAF1 17117 106 + 1
---ACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAACAAACAACAAAGUUGGAAAUUACCUACACGUACAGUGAAAACCAUUCAUGUGUGUCUCGAGUAUUUUAU
---(((((((((..(((((((((........)))))))))....((((...))))..........((((((..((((.....)))).)))))))))))))))....... ( -27.80)
>DroEre_CAF1 17197 109 + 1
CGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAACUAACAACAAAGUUUGAAAUUACCUCCUCGUACAGUGAAAACCAUUCAUGUGCGUCUCGAGUAUUUUAU
...(((((((((..(((((((((........))))))))).............................(((((.((((.....))))))))))))))))))....... ( -28.70)
>DroYak_CAF1 16979 109 + 1
CGAACUUGGGGCAUUUUCUCAAGAGUUUUUCUUUGGGAAACGAACAACAAAGUUUGAAAUUACCUCCUCGUACAGUGAAAACCAUUCAUGUGUGUCUCGAGUAUUUUAU
...((((((((((((((((((((........)))))))))(((((......)))))...............(((.((((.....))))))))))))))))))....... ( -25.50)
>consensus
CGAACUUGGGGCAUUUUCUCAAGAGUUUUUCCUUGGGAAACGAACAACAAAGUUGGAAAUUACCUCCUCGUACAGUGAAAACCAUUCAUGUGUGUCUCGAGUAUUUUAU
...(((((((((..(((((((((........))))))))).............................(((((.((((.....))))))))))))))))))....... (-24.17 = -23.80 +  -0.37)

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 11:07:11 2006