Locus 3214

Sequence ID X_DroMel_CAF1
Location 8,512,344 – 8,512,516
Length 172
Max. P 0.998088
window5270 window5271 window5272 window5273

overview

Window 0

Location 8,512,344 – 8,512,453
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.15
Mean single sequence MFE -37.66
Consensus MFE -18.18
Energy contribution -19.10
Covariance contribution 0.92
Combinations/Pair 1.18
Mean z-score -2.95
Structure conservation index 0.48
SVM decision value 2.95
SVM RNA-class probability 0.997851
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8512344 109 - 22224390
CGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGCCACUGAUUAACCCGCAACUCUGCCCCUUUU-CCC----ACUCUUUUCCCCCACCUCCAC-G-----UAGCCCAUU
.(.(((((((((((.(..(((((.((.((((.......)))).)).)))))..).)))(((....))).))))))-)))----.....................-.-----......... ( -34.80)
>DroSec_CAF1 53529 100 - 1
--------AGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACUCUACCCCUUUU-CCC----ACUCUCUUCCCCCAC-UCCCC-G-----UUGCCCAUA
--------.(((((.(..(((((.(((((((.......)))).))))))))..).)))(((((............-...----...............-.....-)-----))))))... ( -29.15)
>DroSim_CAF1 56734 101 - 1
--------AGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACUCUGCCCCUUUUGCCC----CCUCUUCUCCCCCAC-UCCCC-G-----CAGCCCAUA
--------(((((((...(((((.(((((((.......)))).)))))))).......(((....))).......))))----)))............-.....-.-----......... ( -34.00)
>DroEre_CAF1 60074 109 - 1
UGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACCCUGCCCCCUUU-UCC----ACUCUUUUCUCCCAC-UCCCCGG-----AAUCCCAUA
...((((((((((((...(((((.(((((((.......)))).))))))))(((.....)))....)))))))))-)))----.........(((...-.....))-----)........ ( -43.60)
>DroYak_CAF1 61680 100 - 1
UGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACUCUGCC-CCUUU-UCC----ACU-------UCCAC-UCCCC-G-----AAUCCCAUA
...(((((((((((.(..(((((.(((((((.......)))).))))))))..).)))(((....))).-)))))-)))----...-------.....-.....-.-----......... ( -37.90)
>DroAna_CAF1 86799 117 - 1
CGAUGGCAGGUGGGGUGGAGGGGGGGCGAUCAUUUGUAGGCGCGGCACCGACUGACCCCAAGCCCAAAACCUUCG-CUCCCCAAAGCCCCUCCGCCUC-UUUUC-GAUUUCUUGCCCAAA
(((.(((.((.(((((....(((((((((...((((..(((..((((.....)).))....)))))))....)))-))))))...))))).)))))..-...))-).............. ( -46.50)
>consensus
_GAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACUCUGCCCCUUUU_CCC____ACUCUUUUCCCCCAC_UCCCC_G_____UAGCCCAUA
.........(.(((.(..(((((.(((((((.......)))).))))))))..).))).)............................................................ (-18.18 = -19.10 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,512,375 – 8,512,477
Length 102
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 63.65
Mean single sequence MFE -39.88
Consensus MFE -20.64
Energy contribution -22.57
Covariance contribution 1.94
Combinations/Pair 1.26
Mean z-score -2.50
Structure conservation index 0.52
SVM decision value 3.00
SVM RNA-class probability 0.998088
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8512375 102 + 22224390
-GGGAAAAGGGGCAGAGUUGCGGGUUAAUCAGUGGCGCGCCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCGCCCCCCCCCCUCCAA-----------AUC-----CCUUUU
-(((....(((((.(((..(.(((((..((.(((((.((((.......)))).))))).))..))))).)..)))...)))))...))).....-----------...-----...... ( -42.60)
>DroEre_CAF1 60105 96 + 1
-GGAAAAGGGGGCAGGGUUGCGGGUCAAUCAGUGCCGCGCCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCGCCCC----------------------CUUUUCUUUU
-((((((((((((.((((.(.(((.........(((((........)))))(((((.......))))).....))).))))))))))----------------------)))))))... ( -48.40)
>DroYak_CAF1 61703 105 + 1
-GGAAAAGG-GGCAGAGUUGCGGGUCAAUCAGUGCCGCGCCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCAACCCCA-CCCC-----------AUCCCUCCUUCAUU
-((((((((-.((......))((((...((.(((((.((((.......))))))).)).))...)))))))))))).............-....-----------.............. ( -34.20)
>DroAna_CAF1 86837 117 + 1
GGAGCGAAGGUUUUGGGCUUGGGGUCAGUCGGUGCCGCGCCUACAAAUGAUCGCCCCCCCUCCACCCCACCUGCCAUCGCACUUCUCCA-CCCCUUGGAGGCCCUACCCCCACCCCCU-
((.((((.(((..((((...(((((((((.((((...)))).))...)))......)))).....))))...))).))))...((((((-.....))))))........)).......- ( -34.30)
>consensus
_GGAAAAAGGGGCAGAGUUGCGGGUCAAUCAGUGCCGCGCCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCACCCCCA_CCCC___________AUC_CU_CCCCUUU
.((((((((((((.......((((.....)...(((.((((.......)))))))..)))....))))))))))))........................................... (-20.64 = -22.57 +   1.94)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,512,375 – 8,512,477
Length 102
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 63.65
Mean single sequence MFE -47.90
Consensus MFE -21.60
Energy contribution -22.35
Covariance contribution 0.75
Combinations/Pair 1.28
Mean z-score -2.68
Structure conservation index 0.45
SVM decision value 2.31
SVM RNA-class probability 0.992083
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8512375 102 - 22224390
AAAAGG-----GAU-----------UUGGAGGGGGGGGGGCGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGCCACUGAUUAACCCGCAACUCUGCCCCUUUUCCC-
......-----...-----------.....((..((((((((((.....(.(((.(..(((((.((.((((.......)))).)).)))))..).))).)..))).)))))))..)).- ( -45.20)
>DroEre_CAF1 60105 96 - 1
AAAAGAAAAG----------------------GGGGCGGGUGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACCCUGCCCCCUUUUCC-
....((((((----------------------((((((((.(..(....(((..(...(((((.(((((((.......)))).))))))))..).))).)..))))))))))))))).- ( -51.90)
>DroYak_CAF1 61703 105 - 1
AAUGAAGGAGGGAU-----------GGGG-UGGGGUUGGGUGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACUCUGCC-CCUUUUCC-
.........((((.-----------((((-..(((((((((.((((((((....))))))(((.(((((((.......)))).))))))..)).))))..)))))..))-))..))))- ( -46.50)
>DroAna_CAF1 86837 117 - 1
-AGGGGGUGGGGGUAGGGCCUCCAAGGGG-UGGAGAAGUGCGAUGGCAGGUGGGGUGGAGGGGGGGCGAUCAUUUGUAGGCGCGGCACCGACUGACCCCAAGCCCAAAACCUUCGCUCC
-..(((((((((((.(((((((((.....-)))))...(((....)))..((((((.(.(..((.(((.((.......)))))....))..)).)))))).))))...))))))))))) ( -48.00)
>consensus
AAAAGAG_AG_GAU___________GGGG_UGGGGGAGGGCGAGGAAAAGGGGGCUUUUCGGUAGCCCGCCACUUGUAGGCGCGGCACUGAUUGACCCGCAACCCUGCCCCCUUUCCC_
................................(((..(((...(((...(.(((....(((((.(((((((.......)))).))))))))....))).)...)))....)))..))). (-21.60 = -22.35 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,512,413 – 8,512,516
Length 103
Sequences 3
Columns 108
Reading direction forward
Mean pairwise identity 83.85
Mean single sequence MFE -20.57
Consensus MFE -17.80
Energy contribution -17.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.87
SVM decision value 1.64
SVM RNA-class probability 0.969396
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8512413 103 + 22224390
CCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCGCCCCCCCCCCUCCAAAUC-----CCUUUUCUUUCCUAAUUUGACCCAGCUUAUCCAAGGCGUUGUCAU
.........((.((((....((((((....))))))...)))))).............-----.................((((...((((.....))))...)))). ( -20.30)
>DroEre_CAF1 60143 97 + 1
CCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCGCCCC-----------CUUUUCUUUUCUUUCCUAAUUUGACCCAGCUUAUCCAAGGCGUUGUCAU
.........((((((.....((((((....))))))....))))))..-----------.....................((((...((((.....))))...)))). ( -23.00)
>DroYak_CAF1 61740 107 + 1
CCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCAACCCCA-CCCCAUCCCUCCUUCAUUCGUUCCUAAUUUGACCCAGCUUAUCCAAGGCGUUGUCAU
.......((((.(((.....((((((....))))))....)))....)))-)............................((((...((((.....))))...)))). ( -18.40)
>consensus
CCUACAAGUGGCGGGCUACCGAAAAGCCCCCUUUUCCUCACCCACCCCC__CC__AUC_CU__UCUUUUCUUUCCUAAUUUGACCCAGCUUAUCCAAGGCGUUGUCAU
.........((.(((((.......))))))).................................................((((...((((.....))))...)))). (-17.80 = -17.80 +   0.00)

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 10:53:57 2006