Locus 1127

Sequence ID 3L_DroMel_CAF1
Location 3,292,690 – 3,292,834
Length 144
Max. P 0.960680
window1753 window1754 window1755

overview

Window 3

Location 3,292,690 – 3,292,794
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.73
Mean single sequence MFE -38.98
Consensus MFE -29.08
Energy contribution -27.72
Covariance contribution -1.36
Combinations/Pair 1.27
Mean z-score -2.43
Structure conservation index 0.75
SVM decision value 1.52
SVM RNA-class probability 0.960680
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3292690 104 + 23771897
GGGGGGGGGUACGUUUCGAGAUAACAGCAACACGAGGAGAUUGUGUAAUCGCUUUGGCGAUUGCU------G----------GGCGGGAAUAUGCUGGUCGCGAUGCGGUUUCCCAUACA
(...(((((..(((.(((.(((..((((.((((((.....))))))((((((....)))))))))------)----------((((......)))).))).))).)))..)))))...). ( -39.10)
>DroSec_CAF1 22405 104 + 1
GGGGGAGGGGACAUUUCGAGAUAACAGCAACGCGAGGAGAUUGUGUAAUCGCUUUGGCGAUUGCU------G----------GGCGGGCAUAUGCUGGUCGCGAUGCGGUUUCCCAUACA
(((..((....)..............(((.(((...........((((((((....)))))))).------.----------(((.(((....))).)))))).)))..)..)))..... ( -38.40)
>DroSim_CAF1 23219 104 + 1
GGGGGAGGGGACAUUUCGAGAUAACAGCAACACGAGGAGAUUGUGUAAUCGCUUUGGCGAUUGCU------G----------GGCGGGAAUAUGCUGGUCGCGAUGCGGUUUCCCAUACA
(((..((....)...(((.(((..((((.((((((.....))))))((((((....)))))))))------)----------((((......)))).))).))).....)..)))..... ( -35.90)
>DroEre_CAF1 24431 116 + 1
--GGGAG-GGGCAGUUUGAGAUAACAGCAACACGAGGAGAUUGUGUAAUCGCGUUGGCGAUUGUUGGGGUUGGGAUUGUUGGGGCGGC-AUAUGCUGGUUGCGAUGCUGUUUCCCAUAUA
--(((((-.((((((((..(((..((((.((((((.....))))))((((((....))))))))))..))).))))))))...(((((-((.(((.....)))))))))))))))..... ( -43.40)
>DroYak_CAF1 25103 111 + 1
--GGGAG-GGGCAGUUCGAGAUAACAGCAACACGAGGAGAUUGUGUAAUCGCUUUGGCGAUUGUU------GGGAUUGCUGGGGCGGGAAAAUGCUGGUCGUGAUGCGGUUUUCUAUACA
--(..((-..(((...(((.....(((((((((((.....))))))..((((((..((((((...------..))))))..)))))).....))))).)))...)))..))..)...... ( -38.10)
>consensus
GGGGGAGGGGACAUUUCGAGAUAACAGCAACACGAGGAGAUUGUGUAAUCGCUUUGGCGAUUGCU______G__________GGCGGGAAUAUGCUGGUCGCGAUGCGGUUUCCCAUACA
..(((((...((...(((.(((..(((((((((((.....))))))((((((....))))))..............................)))))))).)))....)))))))..... (-29.08 = -27.72 +  -1.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,292,690 – 3,292,794
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.73
Mean single sequence MFE -24.52
Consensus MFE -20.92
Energy contribution -21.04
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.13
Structure conservation index 0.85
SVM decision value 1.47
SVM RNA-class probability 0.956362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3292690 104 - 23771897
UGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAAUCUCCUCGUGUUGCUGUUAUCUCGAAACGUACCCCCCCCC
.((((((....))...(((.((.(((((..........----------.------...((((((....))))))((((.........)))))))))...)).)))...))))........ ( -23.70)
>DroSec_CAF1 22405 104 - 1
UGUAUGGGAAACCGCAUCGCGACCAGCAUAUGCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAAUCUCCUCGCGUUGCUGUUAUCUCGAAAUGUCCCCUCCCCC
.....((((....((((..(((.(((((.((((..((.----------.------.))((((((....)))))).............))))))))).....)))..))))....)))).. ( -26.90)
>DroSim_CAF1 23219 104 - 1
UGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAAUCUCCUCGUGUUGCUGUUAUCUCGAAAUGUCCCCUCCCCC
.....((((....((((..(((...((........)).----------(------(((((((((....))))))((((.........)))).)))).....)))..))))....)))).. ( -25.20)
>DroEre_CAF1 24431 116 - 1
UAUAUGGGAAACAGCAUCGCAACCAGCAUAU-GCCGCCCCAACAAUCCCAACCCCAACAAUCGCCAACGCGAUUACACAAUCUCCUCGUGUUGCUGUUAUCUCAAACUGCCC-CUCCC--
....((((((((((((.(((.....((....-))........................((((((....)))))).............))).))))))).)))))........-.....-- ( -25.50)
>DroYak_CAF1 25103 111 - 1
UGUAUAGAAAACCGCAUCACGACCAGCAUUUUCCCGCCCCAGCAAUCCC------AACAAUCGCCAAAGCGAUUACACAAUCUCCUCGUGUUGCUGUUAUCUCGAACUGCCC-CUCCC--
.....(((.(((.(((.(((((..((.(((.....((....))......------...((((((....))))))....)))))..))))).))).))).)))..........-.....-- ( -21.30)
>consensus
UGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC__________C______AGCAAUCGCCAAAGCGAUUACACAAUCUCCUCGUGUUGCUGUUAUCUCGAAAUGUCCCCUCCCCC
....((((((((.(((.(((((...((........)).....................((((((....))))))...........))))).))).))).)))))................ (-20.92 = -21.04 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,292,730 – 3,292,834
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.10
Mean single sequence MFE -26.00
Consensus MFE -18.16
Energy contribution -18.56
Covariance contribution 0.40
Combinations/Pair 1.17
Mean z-score -2.16
Structure conservation index 0.70
SVM decision value 1.04
SVM RNA-class probability 0.905007
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3292730 104 - 23771897
ACCUAUGAUGCACUACACUCUGCGAUUGGACAGAACUCAUUGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAA
......(((((.........((((((.((......)).)))))).((....)))))))((.....((........)).----------.------.))((((((....))))))...... ( -25.10)
>DroSec_CAF1 22445 104 - 1
ACCUAUGAUGCACUACACGCUACGAUUGGACAGAACCCAUUGUAUGGGAAACCGCAUCGCGACCAGCAUAUGCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAA
......(((((.........((((((.((......)).)))))).((....)))))))(((..((.....))..))).----------.------.(.((((((....)))))).).... ( -28.30)
>DroSim_CAF1 23259 104 - 1
ACCUAUGAUGCACUACACUCUACGAUUGGACAGAACCCAUUGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC----------C------AGCAAUCGCCAAAGCGAUUACACAA
......(((((.........((((((.((......)).)))))).((....)))))))((.....((........)).----------.------.))((((((....))))))...... ( -26.90)
>DroEre_CAF1 24468 119 - 1
AAAUAUGAUGCACUAAACUCUGCGAUUGGAUUGAAUCGCCUAUAUGGGAAACAGCAUCGCAACCAGCAUAU-GCCGCCCCAACAAUCCCAACCCCAACAAUCGCCAACGCGAUUACACAA
......(((((..........((((((......)))))).......(....).)))))((.....))....-..........................((((((....))))))...... ( -23.10)
>DroYak_CAF1 25140 114 - 1
AGCUAUGAUGCACUAAACUGUGCGAUUGGAUAGACUCCACUGUAUAGAAAACCGCAUCACGACCAGCAUUUUCCCGCCCCAGCAAUCCC------AACAAUCGCCAAAGCGAUUACACAA
.(((.((((((......(((((((..((((.....)))).)))))))......))))))......((........))...)))......------...((((((....))))))...... ( -26.60)
>consensus
ACCUAUGAUGCACUACACUCUGCGAUUGGACAGAACCCAUUGUAUGGGAAACCGCAUCGCGACCAGCAUAUUCCCGCC__________C______AGCAAUCGCCAAAGCGAUUACACAA
.....((((((.........((((((.((......)).)))))).((....))))))))......((........)).....................((((((....))))))...... (-18.16 = -18.56 +   0.40)

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 09:59:50 2006