Locus 6414

Sequence ID 2R_DroMel_CAF1
Location 20,053,601 – 20,053,754
Length 153
Max. P 0.956438
window10232 window10233 window10234

overview

Window 2

Location 20,053,601 – 20,053,719
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.30
Mean single sequence MFE -32.16
Consensus MFE -18.29
Energy contribution -18.22
Covariance contribution -0.07
Combinations/Pair 1.32
Mean z-score -1.39
Structure conservation index 0.57
SVM decision value 0.02
SVM RNA-class probability 0.544080
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20053601 118 + 20766785
CGAUGACGA--UCGGUGUUGAAAUGAAGUGCGCAAUCGGAGGCAAAGGCAUUGAGGAGAAACACCAGCUUCCAAGUUGCCAAUUGAUGGCAGGGAGAAUCGAAUGCAGAUAUUCGGGUCA
.......((--((((((((.......(((((((........))....))))).......))))))..(((((....(((((.....))))))))))...((((((....)))))))))). ( -32.44)
>DroSec_CAF1 13368 118 + 1
CGAUGACGA--UCGGUGUUGAAAUGAAGUGCGCAAUCGGAGGCAGACGCAUUGAGGAGGAGCAGCGGCUCCCAAGUUGCCAAUUGAUGGGAGGGAGAAUCGAAUGCAGACAUUCGGGUCA
...((((..--(((.((((.......((((((...((.......)))))))).......)))).)))(((((....(.(((.....))).))))))..(((((((....))))))))))) ( -31.24)
>DroSim_CAF1 13718 118 + 1
CGAUGACGA--UCGGUGUUGAAAUGGAGUGCGCAAUCGGAGACAGACGCAUUGAGGAGGAGCAGCGGUUCCCAAGUUGCCAAUUGAUGGGGGGAAGAAUCGAAUGCAGACAUUCGGGUCA
...((((((--(((.((((....(..((((((...(((....).))))))))..)....)))).)))))(((..(((.......)))..)))......(((((((....))))))))))) ( -31.20)
>DroEre_CAF1 13625 108 + 1
CGAUGACGA--UCGGUGUUGAAAUGGAGUGCGCAAUCGGA------CGCCACGAGGAGGAGCAGCAGCUCCCCAGUUGCCAACUGAA----GAGGAAAUUGAAUGGAGACAUUCAGGUCA
((((..((.--((.((......)).))...))..))))((------(((.((..((.(((((....))))))).)).))........----.......(((((((....)))))))))). ( -35.90)
>DroYak_CAF1 13683 108 + 1
CGAUGACGA--UCGGUGUUGAAAUGGAGUGCGCAAUCGGA------CGCCAAGAGGAGGAGCAGCAGCUCCCCAGUUGCCAGUUGAA----GGGGAAACUGAAUGGAGACAUUCAGGUCA
.(((..(((--(.(((.......(((.((.((....)).)------).)))...((.(((((....)))))))....))).))))..----.......(((((((....)))))))))). ( -38.70)
>DroAna_CAF1 15691 93 + 1
UGAUGACUAAACUGGCCGAGAAGUAAAG-------UUGAAGACAG-----UUGAGUUGAAAC-----------AGACGUCAAUUGAA----AGGAAAAUUGAAUGGAAACAUUCAGGUCA
.............((((...........-------.......(((-----(((((((.....-----------.))).)))))))..----........((((((....)))))))))). ( -23.50)
>consensus
CGAUGACGA__UCGGUGUUGAAAUGAAGUGCGCAAUCGGAG_CAG_CGCAUUGAGGAGGAGCAGCAGCUCCCAAGUUGCCAAUUGAA____GGGAAAAUCGAAUGCAGACAUUCAGGUCA
...((((......(((.............(((..............)))........(((((....)))))......)))..................(((((((....))))))))))) (-18.29 = -18.22 +  -0.07)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,053,639 – 20,053,754
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.48
Mean single sequence MFE -30.20
Consensus MFE -18.30
Energy contribution -18.02
Covariance contribution -0.28
Combinations/Pair 1.32
Mean z-score -1.40
Structure conservation index 0.61
SVM decision value 0.70
SVM RNA-class probability 0.827584
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20053639 115 + 20766785
GGCAAAGGCAUUGAGGAGAAACACCAGCUUCCAAGUUGCCAAUUGAUGGCAGGGAGAAUCGAAUGCAGAUAUUCGGGUCAAUUGACAACGCAGAGAAUCAAUAGUACGAUCUCAG-----
.((....(((((((((.......))..(((((....(((((.....))))))))))..)).)))))..........(((....)))...)).((((.((........))))))..----- ( -26.70)
>DroSec_CAF1 13406 115 + 1
GGCAGACGCAUUGAGGAGGAGCAGCGGCUCCCAAGUUGCCAAUUGAUGGGAGGGAGAAUCGAAUGCAGACAUUCGGGUCAAUUGACAUGUCAGAGAAUCCAAAGUACGAACUCAG-----
.((....))..(((((.(((((....))))))...((.(((.....))).))(((((..((((((....))))))..))..((((....))))....)))..........)))).----- ( -29.10)
>DroSim_CAF1 13756 115 + 1
GACAGACGCAUUGAGGAGGAGCAGCGGUUCCCAAGUUGCCAAUUGAUGGGGGGAAGAAUCGAAUGCAGACAUUCGGGUCAAUUGACAUGUCAGAGAAUCCAAAGUACGAACUCAG-----
((((...(((.....(.(((((....))))))....)))((((((((...........(((((((....)))))))))))))))...)))).(((..((........)).)))..----- ( -26.40)
>DroEre_CAF1 13663 105 + 1
------CGCCACGAGGAGGAGCAGCAGCUCCCCAGUUGCCAACUGAA----GAGGAAAUUGAAUGGAGACAUUCAGGUCAAUUGACAAGCCAGAGCAUCUGUAGUCCGAUCUUAG-----
------.((.((..((.(((((....))))))).)).))......((----(((((..(((((((....)))))))(((....)))....(((.....)))...)))..))))..----- ( -32.10)
>DroYak_CAF1 13721 105 + 1
------CGCCAAGAGGAGGAGCAGCAGCUCCCCAGUUGCCAGUUGAA----GGGGAAACUGAAUGGAGACAUUCAGGUCAACUGAAAAGUCAGAGAAUCCGCAGUCCGAUCUUAG-----
------....((((((.(((((....)))))))..(((((((((((.----.......(((((((....))))))).)))))))........(......))))).....))))..----- ( -34.40)
>DroAna_CAF1 15724 100 + 1
GACAG-----UUGAGUUGAAAC-----------AGACGUCAAUUGAA----AGGAAAAUUGAAUGGAAACAUUCAGGUCAAUUGACAUGUCUGAAGCUGGCAAAUCAAAUCAUUGAUUGG
..(((-----(..(.((((..(-----------(((((((((((((.----.......(((((((....))))))).)))))))))..)))))..(....)...))))....)..)))). ( -32.50)
>consensus
G_CAG_CGCAUUGAGGAGGAGCAGCAGCUCCCAAGUUGCCAAUUGAA____GGGAAAAUCGAAUGCAGACAUUCAGGUCAAUUGACAAGUCAGAGAAUCCAAAGUACGAUCUCAG_____
............(((..(((((....)))))........(((((((............(((((((....))))))).)))))))..........................)))....... (-18.30 = -18.02 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,053,639 – 20,053,754
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.48
Mean single sequence MFE -28.26
Consensus MFE -17.61
Energy contribution -17.61
Covariance contribution 0.00
Combinations/Pair 1.32
Mean z-score -1.70
Structure conservation index 0.62
SVM decision value 1.47
SVM RNA-class probability 0.956438
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20053639 115 - 20766785
-----CUGAGAUCGUACUAUUGAUUCUCUGCGUUGUCAAUUGACCCGAAUAUCUGCAUUCGAUUCUCCCUGCCAUCAAUUGGCAACUUGGAAGCUGGUGUUUCUCCUCAAUGCCUUUGCC
-----..(((((((......))).)))).((((((((((((((..(((((......)))))...(.....)...))))))))))))..((((((....)))))).......))....... ( -26.80)
>DroSec_CAF1 13406 115 - 1
-----CUGAGUUCGUACUUUGGAUUCUCUGACAUGUCAAUUGACCCGAAUGUCUGCAUUCGAUUCUCCCUCCCAUCAAUUGGCAACUUGGGAGCCGCUGCUCCUCCUCAAUGCGUCUGCC
-----..(((((((.....)))))))...(((.((((((((((..((((((....)))))).............))))))))))....((((((....)))))).........))).... ( -31.86)
>DroSim_CAF1 13756 115 - 1
-----CUGAGUUCGUACUUUGGAUUCUCUGACAUGUCAAUUGACCCGAAUGUCUGCAUUCGAUUCUUCCCCCCAUCAAUUGGCAACUUGGGAACCGCUGCUCCUCCUCAAUGCGUCUGUC
-----..(((((((.....)))))))...(((.((((((((((...(((((....)))))((....))......))))))))))....((((........)))).........))).... ( -27.00)
>DroEre_CAF1 13663 105 - 1
-----CUAAGAUCGGACUACAGAUGCUCUGGCUUGUCAAUUGACCUGAAUGUCUCCAUUCAAUUUCCUC----UUCAGUUGGCAACUGGGGAGCUGCUGCUCCUCCUCGUGGCG------
-----.........(.((((.........((.(((((((((((..((((((....))))))........----.)))))))))))))(((((((....)))))))...))))).------ ( -30.40)
>DroYak_CAF1 13721 105 - 1
-----CUAAGAUCGGACUGCGGAUUCUCUGACUUUUCAGUUGACCUGAAUGUCUCCAUUCAGUUUCCCC----UUCAACUGGCAACUGGGGAGCUGCUGCUCCUCCUCUUGGCG------
-----((((((..((((.((((.((((((...((.((((((((.(((((((....))))))).......----.)))))))).))..)))))))))).).)))...))))))..------ ( -32.70)
>DroAna_CAF1 15724 100 - 1
CCAAUCAAUGAUUUGAUUUGCCAGCUUCAGACAUGUCAAUUGACCUGAAUGUUUCCAUUCAAUUUUCCU----UUCAAUUGACGUCU-----------GUUUCAACUCAA-----CUGUC
........(((.((((...........(((((..(((((((((..((((((....))))))........----.)))))))))))))-----------)..)))).))).-----..... ( -20.82)
>consensus
_____CUAAGAUCGGACUUUGGAUUCUCUGACAUGUCAAUUGACCCGAAUGUCUCCAUUCAAUUCUCCC____AUCAAUUGGCAACUUGGGAGCUGCUGCUCCUCCUCAAUGCG_CUG_C
.................................((((((((((..((((((....)))))).............))))))))))....((((((....))))))................ (-17.61 = -17.61 +   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 12:10:24 2006