Locus 1292

Sequence ID 3R_DroMel_CAF1
Location 3,817,298 – 3,817,436
Length 138
Max. P 0.956670
window2108 window2109

overview

Window 8

Location 3,817,298 – 3,817,402
Length 104
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 90.13
Mean single sequence MFE -32.82
Consensus MFE -25.74
Energy contribution -25.02
Covariance contribution -0.72
Combinations/Pair 1.24
Mean z-score -1.44
Structure conservation index 0.78
SVM decision value 0.04
SVM RNA-class probability 0.551528
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3817298 104 - 27905053
CAUGUUGCUGGCGCGUUUUU-UUCCGAACUCGGUUAGGAAAUCGCCUGCGAUUUCAAUCGCGUGCAAGUCGCGCGCAGUCUGGUAUUCGCUUGAAAGUUUAAAAA
...(((((.((((.((((((-(.(((....)))..))))))))))).))))).......((((((.....))))))..((.(((....))).))........... ( -31.60)
>DroSec_CAF1 45271 104 - 1
CAUGUUGCUGGCGCGUUUUU-UUCCGAACUCGGUUAGGAAAUCGCCUGCGAUUUCAAUCGCGUGCAAGUCGCGCGCUUCCUGGUAUUCGCUUGAAAGUUUAAAAA
....((((.((((.((((((-(.(((....)))..))))))))))).))))(((((...((((((.....)))))).....(((....))))))))......... ( -31.00)
>DroSim_CAF1 49788 104 - 1
CAUGUUGCUGGCGCGUUUUU-UUCCGAACUCGGUUAGGAAAUCGCCUGCGAUUUCAAUCGCGUGCAAGUCGCGCGCUACCUGGUAUUCGCUUGAAAGUUUAAAAA
....((((.((((.((((((-(.(((....)))..))))))))))).))))((((((.(((((((.....))))))(((...)))...).))))))......... ( -31.20)
>DroEre_CAF1 36615 104 - 1
CAUGUUGCUGCCGCGUUUUU-UCCCGAGCUUGAUUGAGAAAUCGCCAGCGAUUUCGAUCGCGUGCAAGUCGCGCGCAGCUCGGUAUUCGCUGGAAAGUUUAAAAA
......(((.(((((..(..-..(((((((.((((((..(((((....)))))))))))((((((.....))))))))))))).)..))).))..)))....... ( -38.40)
>DroYak_CAF1 49333 105 - 1
CAUGUUGCUGGCGCGUUUUUUUCGUGAGCUUGGUUAAGAAAUCGUCAGCGAUUUCGAUCGCGUGCAAGUCGCGCGCAGCUUGGUAUUUGCUUGAAAGUUGAAAAA
....(((((((((..((((..(((......)))..))))...)))))))))(((((((.((((((.....))))))(((.........))).....))))))).. ( -31.90)
>consensus
CAUGUUGCUGGCGCGUUUUU_UUCCGAACUCGGUUAGGAAAUCGCCUGCGAUUUCAAUCGCGUGCAAGUCGCGCGCAGCCUGGUAUUCGCUUGAAAGUUUAAAAA
......(((((((.((((((...(((....)))...)))))))))).((((..(((...((((((.....))))))....)))...)))).....)))....... (-25.74 = -25.02 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,817,338 – 3,817,436
Length 98
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.36
Mean single sequence MFE -26.05
Consensus MFE -13.39
Energy contribution -14.58
Covariance contribution 1.20
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.51
SVM decision value 1.47
SVM RNA-class probability 0.956670
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3817338 98 + 27905053
GCACGCGAUUGAAAUCGCAGGCGAUUUCCUAACC-------GAGUUCGGAA-AAAAACGCGCCAGCAACAU--------GUGCACCAAAUGCACUUGCCACACCGCAACAAUAA---
((.((((...(((((((....)))))))....((-------(....)))..-.....))))...((((...--------(((((.....)))))))))......))........--- ( -28.10)
>DroSec_CAF1 45311 98 + 1
GCACGCGAUUGAAAUCGCAGGCGAUUUCCUAACC-------GAGUUCGGAA-AAAAACGCGCCAGCAACAU--------GUGCAGCAUAUGCACUUGCCACACAACAACAACAC---
((..(((((....))))).((((.........((-------(....)))..-.......)))).))..((.--------(((((.....))))).)).................--- ( -26.77)
>DroSim_CAF1 49828 98 + 1
GCACGCGAUUGAAAUCGCAGGCGAUUUCCUAACC-------GAGUUCGGAA-AAAAACGCGCCAGCAACAU--------GUGCAGCAUAUGCACUUGCCACACAACAACAACAC---
((..(((((....))))).((((.........((-------(....)))..-.......)))).))..((.--------(((((.....))))).)).................--- ( -26.77)
>DroEre_CAF1 36655 98 + 1
GCACGCGAUCGAAAUCGCUGGCGAUUUCUCAAUC-------AAGCUCGGGA-AAAAACGCGGCAGCAACAU--------GUGCAGCAAAUGCACUUGCCACACAGCAACAACGC---
....(((...(....)(((((((.((((((....-------......))))-))...)))(((((......--------(((((.....))))))))))...)))).....)))--- ( -27.10)
>DroYak_CAF1 49373 99 + 1
GCACGCGAUCGAAAUCGCUGACGAUUUCUUAACC-------AAGCUCACGAAAAAAACGCGCCAGCAACAU--------GUGCAGCAUAUGCACUUGCCACACAGCAACAACAC---
((.((((...(((((((....)))))))......-------..(....)........))))...((((...--------(((((.....)))))))))......))........--- ( -22.00)
>DroPer_CAF1 20381 106 + 1
GCACGCGAUUUAAAACGC--GCCAUUUCGUCAUACGCUCAUGUGUACGUAA-AGCGAAGCAACAACCACAUCGAAACACUUGUU------GCACUUGGUGCAC--CAACAACACCAA
................((--((((.(((((..((((..(....)..)))).-.)))))(((((((..............)))))------))...))))))..--............ ( -25.54)
>consensus
GCACGCGAUUGAAAUCGCAGGCGAUUUCCUAACC_______GAGUUCGGAA_AAAAACGCGCCAGCAACAU________GUGCAGCAUAUGCACUUGCCACACAGCAACAACAC___
....(((((....))))).(((((..................................((....)).............(((((.....)))))))))).................. (-13.39 = -14.58 +   1.20)

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 10:05:50 2006