Locus 2849

Sequence ID 2L_DroMel_CAF1
Location 8,167,231 – 8,167,388
Length 157
Max. P 0.805489
window4530 window4531 window4532

overview

Window 0

Location 8,167,231 – 8,167,348
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.10
Mean single sequence MFE -31.61
Consensus MFE -27.04
Energy contribution -27.08
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -1.30
Structure conservation index 0.86
SVM decision value 0.18
SVM RNA-class probability 0.620141
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8167231 117 + 22407834
UGUACGUCAUUUGACAAGCCCCACCGUCAUUUGAAUAAAAUGCGCCCCGUUUCAGGGCCAAAACCUGUUGACUCAACUAUGUC---CUAUCCCUCGGGUCGAGUUGAGUCAACUAUUUGG
.(((..(((..((((..........))))..)))......)))((((.......))))((((....((((((((((((.((.(---((.......))).))))))))))))))..)))). ( -35.90)
>DroSec_CAF1 7107 116 + 1
UGUACGUCAUUUGACAAGCCCCACCUUCAUUUGAAUAAAAUGCGCCCCGUUUCAGGGCCAAAACCUGUUGACUCAACUAUG----UGUAUCCCUCGGGUCGAGUUGAGUCAACUAUUUGG
.....(((....)))...............(..((((...((.((((.......))))))......((((((((((((.((----.....((....)).))))))))))))))))))..) ( -31.50)
>DroSim_CAF1 7624 120 + 1
UGUACGUCAUUUGACAAGCCCCACCUUCAUUUGAAUAAAUUGUGCCCCGUUUCAGGGCCAAAACCUGUUGACUCAACUAUGUAUGUAUAUCCCUCGGGUCGAGUUGAGUCAACUAUUUGG
.(((((((....)))..........(((....)))......))))(((......)))(((((....((((((((((((............((....))...))))))))))))..))))) ( -31.96)
>DroEre_CAF1 7620 112 + 1
UGUACGUCCUUUGACAAGCCCCACCUUCGUUUAAAUGAAAUGCGCUCCGUUUCAGGGCCAAAACCUGUUGACUCAACU--------GUAUCCCUCGGGUCGAGCUGAGCCAACUAUUUGG
.....(((((..(((.(((..((..(((((....))))).)).)))..)))..)))))((((....((((.((((.((--------..((((...))))..)).)))).))))..)))). ( -25.30)
>DroYak_CAF1 7287 115 + 1
UGUACGUCAUUUGACAAGCCCCACCUUCAUUUGAAUGAAAUGCGCCCCGUUUCAGGGCCAAAACCUGUUGCCUCAGCUA-G----UAUAUCCCUCGGGUCGGGCUGAGUCAACUAUUUGG
.....(((....)))..((((....(((....)))(((((((.....)))))))))))((((....((((.(((((((.-.----.....((....))...))))))).))))..)))). ( -33.40)
>consensus
UGUACGUCAUUUGACAAGCCCCACCUUCAUUUGAAUAAAAUGCGCCCCGUUUCAGGGCCAAAACCUGUUGACUCAACUAUG____UAUAUCCCUCGGGUCGAGUUGAGUCAACUAUUUGG
.....(((....))).....(((.................((.((((.......))))))......((((((((((((............((....))...))))))))))))....))) (-27.04 = -27.08 +   0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,167,231 – 8,167,348
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.10
Mean single sequence MFE -35.24
Consensus MFE -30.54
Energy contribution -30.62
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.43
Structure conservation index 0.87
SVM decision value 0.63
SVM RNA-class probability 0.805489
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8167231 117 - 22407834
CCAAAUAGUUGACUCAACUCGACCCGAGGGAUAG---GACAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCAUUUUAUUCAAAUGACGGUGGGGCUUGUCAAAUGACGUACA
.......((((((((((((....((........)---)....))))))))))))(((((..(((((((...))))))((((((.....))))).)..)..)))))(((....)))..... ( -37.20)
>DroSec_CAF1 7107 116 - 1
CCAAAUAGUUGACUCAACUCGACCCGAGGGAUACA----CAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCAUUUUAUUCAAAUGAAGGUGGGGCUUGUCAAAUGACGUACA
.......((((((((((((...((....)).....----...))))))))))))(((((..(((((((...)))))).(((((.....)))))....)..)))))(((....)))..... ( -34.80)
>DroSim_CAF1 7624 120 - 1
CCAAAUAGUUGACUCAACUCGACCCGAGGGAUAUACAUACAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCACAAUUUAUUCAAAUGAAGGUGGGGCUUGUCAAAUGACGUACA
(((....(((((((((((....((....)).(((......)))))))))))))).....(((((((((...)))))).)))................))).(..((((....))))..). ( -34.60)
>DroEre_CAF1 7620 112 - 1
CCAAAUAGUUGGCUCAGCUCGACCCGAGGGAUAC--------AGUUGAGUCAACAGGUUUUGGCCCUGAAACGGAGCGCAUUUCAUUUAAACGAAGGUGGGGCUUGUCAAAGGACGUACA
(((((..((((((((((((...((....))....--------))))))))))))....))))).(((...(((.(((.(.((((........))))...).))))))...)))....... ( -34.20)
>DroYak_CAF1 7287 115 - 1
CCAAAUAGUUGACUCAGCCCGACCCGAGGGAUAUA----C-UAGCUGAGGCAACAGGUUUUGGCCCUGAAACGGGGCGCAUUUCAUUCAAAUGAAGGUGGGGCUUGUCAAAUGACGUACA
........(((((..(((((..((((((((...((----.-.((((..(....).)))).)).))))....)))).(((.((((((....)))))))))))))).))))).......... ( -35.40)
>consensus
CCAAAUAGUUGACUCAACUCGACCCGAGGGAUACA____CAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCAUUUUAUUCAAAUGAAGGUGGGGCUUGUCAAAUGACGUACA
(((....((((((((((((...((....))............))))))))))))......((((((((...)))))).)).................))).(..((((....))))..). (-30.54 = -30.62 +   0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,167,271 – 8,167,388
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.18
Mean single sequence MFE -36.17
Consensus MFE -27.98
Energy contribution -28.33
Covariance contribution 0.35
Combinations/Pair 1.17
Mean z-score -1.39
Structure conservation index 0.77
SVM decision value -0.05
SVM RNA-class probability 0.508958
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8167271 117 - 22407834
CGGGCGGUCCUUCGGAUUACGACCUGACAUUAACAUGCUUCCAAAUAGUUGACUCAACUCGACCCGAGGGAUAG---GACAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCA
((((((((((...))))..)).)))).........(((...((((..((((((((((((....((........)---)....))))))))))))....))))((((((...))))))))) ( -40.70)
>DroSec_CAF1 7147 116 - 1
CGGGCGGUCCUUCGGAUUACGACCUGACAUUAACAUGCUUCCAAAUAGUUGACUCAACUCGACCCGAGGGAUACA----CAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCA
((((((((((...))))..)).)))).........(((...((((..((((((((((((...((....)).....----...))))))))))))....))))((((((...))))))))) ( -38.60)
>DroSim_CAF1 7664 120 - 1
CGGGCGGUCCUUCGGAUUACGACCUGACAUUAACAUGCUUCCAAAUAGUUGACUCAACUCGACCCGAGGGAUAUACAUACAUAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCACA
((((((((((...))))..)).))))...............((((..(((((((((((....((....)).(((......))))))))))))))....))))((((((...))))))... ( -36.40)
>DroEre_CAF1 7660 112 - 1
CAGGCGGUCCCUAGGAUUACGACCUGACAUUAACAUGCUACCAAAUAGUUGGCUCAGCUCGACCCGAGGGAUAC--------AGUUGAGUCAACAGGUUUUGGCCCUGAAACGGAGCGCA
...(((.(((.((((..((.((((((..........((((.....))))((((((((((...((....))....--------)))))))))).)))))).))..))))....))).))). ( -39.30)
>DroYak_CAF1 7327 115 - 1
CAGGCGGUCCUUAGGAUUACGACCUGACAUUAACAUGCUUCCAAAUAGUUGACUCAGCCCGACCCGAGGGAUAUA----C-UAGCUGAGGCAACAGGUUUUGGCCCUGAAACGGGGCGCA
((((((((((...))))..)).)))).........(((...((((..((((.((((((....((....)).....----.-..)))))).))))....))))((((((...))))))))) ( -35.70)
>DroAna_CAF1 8684 94 - 1
CAGGAGGUCCUUAGGAUUACGACCUGACAUUAACAUGCCUGCAAAUAGUUGACGCAACAUGGCUUGAUGGAUGG--------CGUUGAGUCAACAGGUUGAG------------------
.....(((((...))))).(((((((.........(((...(((....)))..)))...(((((..(((.....--------)))..))))).)))))))..------------------ ( -26.30)
>consensus
CAGGCGGUCCUUAGGAUUACGACCUGACAUUAACAUGCUUCCAAAUAGUUGACUCAACUCGACCCGAGGGAUAC_____C_UAGUUGAGUCAACAGGUUUUGGCCCUGAAACGGGGCGCA
((((((((((...))))..)).)))).....................((((((((((((...((....))............))))))))))))........(((((.....)))))... (-27.98 = -28.33 +   0.35)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:51 2006