Locus 5998

Sequence ID 2L_DroMel_CAF1
Location 16,897,045 – 16,897,316
Length 271
Max. P 0.948839
window9526 window9527 window9528

overview

Window 6

Location 16,897,045 – 16,897,165
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.90
Mean single sequence MFE -44.44
Consensus MFE -37.96
Energy contribution -38.20
Covariance contribution 0.24
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.85
SVM decision value 1.39
SVM RNA-class probability 0.948839
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16897045 120 - 22407834
UGCUACACAUUCCAGCGGCCACCGAGGAGCAGCUGCGAGAGAUCUUCUCCAGUUGCGGCGAAAUAGACUACAUUCGCUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGAGUAGCAUACG
((((((....(((.((((((.((.(((.(((((((.(((((...))))))))))))((((((..........)))))).)))...)).((....))..))))))...))))))))).... ( -47.50)
>DroSec_CAF1 9753 120 - 1
UGCUACUCAUUCCAGCGGCCACCGAGGAGCAGCUGCGAGAGAUCUUCUCAAGUUGUGGCGAAAUAGACUACAUACGCUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGAGUAGCAUACG
((((((((......((((((.((..((.(((((...(((((...)))))..((((((((......).))))).)))))))))...)).((....))..))))))....)))))))).... ( -46.90)
>DroSim_CAF1 12024 120 - 1
UGCUACUCAUUCCAGCGGCCACCGAGGAGCAGCUGCGAGAGAUCUUCUCCAGUUGUGGCGAAAUAGACUACAUACGUUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGAGUAGCAUACG
((((((((......((((((..((....(((((((.(((((...))))))))))))..))...............((((((........))))))...))))))....)))))))).... ( -49.00)
>DroEre_CAF1 11680 117 - 1
U-CUAC--CAUCCAGCGGCCAACGAGGAGCAGUUGCGCGAGAUCUUCUCCAGCUGCGGCGAGAUAGACUACAUACGCUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGGGUAGCAUACG
.-((((--(.....((((((..((....(((((((...(((.....))))))))))..))..............(((((((....)).))))).....)))))).....)))))...... ( -39.80)
>DroYak_CAF1 9585 117 - 1
U-CUAA--UAUCCAGCGGCCACCGAGGAGCAGCUGCGCGAGAUCUUCUCCAGCUGCGGCGAGAUAGACUACAUACGCUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGAGUAGCAUACG
.-(((.--..(((.((((((..((....(((((((...(((.....))))))))))..))..............(((((((....)).))))).....))))))...))).)))...... ( -39.00)
>consensus
UGCUAC_CAUUCCAGCGGCCACCGAGGAGCAGCUGCGAGAGAUCUUCUCCAGUUGCGGCGAAAUAGACUACAUACGCUGCCUGCAGGAUGGCGACAAGGGCUGCAAAGGAGUAGCAUACG
((((((....(((.((((((..((....(((((((.(((((...))))))))))))..))..............(((((((....)).))))).....))))))...))))))))).... (-37.96 = -38.20 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,897,165 – 16,897,276
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.04
Mean single sequence MFE -27.33
Consensus MFE -23.34
Energy contribution -23.62
Covariance contribution 0.28
Combinations/Pair 1.13
Mean z-score -1.84
Structure conservation index 0.85
SVM decision value 0.98
SVM RNA-class probability 0.895071
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16897165 111 + 22407834
CAUGAUGUUAGCAUUUAGUUAAAACUACUUACU--G-------CUUUACUUACAGUACUUUAGGCUGCCAACGAAAAUGGUUCGCUUGGCAUCCUUGUCACUGGGCUGCUUAUCCUUUGC
...((((.((((...((((....))))......--.-------.........((((((...(((.((((((((((.....)))).)))))).))).)).)))).))))..))))...... ( -27.40)
>DroSec_CAF1 9873 111 + 1
CUUAACGUUAGCACUUAGUUAAAACUACUGACU--U-------CUUUACUUACAGUACUUUAGGCUGCCAACGAAAAUGGUUCGCUUGGCAUCCUUGUCACUGGGCUGCUGAUCCUUUCC
......(((((((((((((..(((.(((((...--.-------.........))))).)))(((.((((((((((.....)))).)))))).)))....)))))).)))))))....... ( -30.12)
>DroSim_CAF1 12144 111 + 1
CUUAAUGUUAGCACUUAGUUCAAACUACUGACU--U-------CUUUACUUACAGUACUUUAGGCUGCCAACGAAAAUGGUUCGCUUGGCAUCCUUGUCACUGGGCUGCUGAUCCUUUCC
......(((((((((((((.(((..(((((...--.-------.........))))).....((.((((((((((.....)))).)))))).)))))..)))))).)))))))....... ( -30.02)
>DroEre_CAF1 11797 111 + 1
UUUAAUAUUAGCACUUUGUUAAAACUACUCUAU--U-------UAUUACUUACAGUAUUUUAGGCUGCCCACGAAAAUGGUUCGCUUGGCAUCCUUGUCAUUGGGCUGUUCAUCCUUUCC
.......(((((.....))))).......(((.--.-------...(((.....)))...)))((.(((((((((.....))))..(((((....))))).))))).))........... ( -18.30)
>DroYak_CAF1 9702 120 + 1
UUUAAUGUUAGCAUGUAGUUAAAACUACUCAAAAGUCAAGGAACGAUACUUACAGUAUUUUAGGCUGCCCACGAAUAUGGUUCGCUUGGCAUCCUUGUCACUGGGCUGCUGAUCCGCUCC
.........(((..(((((....)))))...........(((.((((((.....)))))...(((.((((((((((...)))))..(((((....))))).))))).)))).)))))).. ( -30.80)
>consensus
CUUAAUGUUAGCACUUAGUUAAAACUACUCACU__U_______CUUUACUUACAGUACUUUAGGCUGCCAACGAAAAUGGUUCGCUUGGCAUCCUUGUCACUGGGCUGCUGAUCCUUUCC
......(((((((..((((....)))).........................((((((...(((.((((((((((.....)))).)))))).))).)).))))...)))))))....... (-23.34 = -23.62 +   0.28)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,897,199 – 16,897,316
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.32
Mean single sequence MFE -40.08
Consensus MFE -32.20
Energy contribution -33.04
Covariance contribution 0.84
Combinations/Pair 1.09
Mean z-score -1.51
Structure conservation index 0.80
SVM decision value 0.21
SVM RNA-class probability 0.634656
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16897199 117 - 22407834
GCGGGUGACUCCCGCGUCUAUGGCGGAGAAAUUCGGCCAGGCAAAGGAUAAGCAGCCCAGUGACAAGGAUGCCAAGCGAACCAUUUUCGUUGGCAGCCUAAAGUACUGUAAGUAAAG---
(((((.....))))).....(((((((....))).))))(((............)))(((((...(((.((((((.((((.....)))))))))).)))....))))).........--- ( -40.90)
>DroSec_CAF1 9907 117 - 1
GCGGGUGACGCCCGCGUCUAUGGCGGAGAAGUUCGGCCAGGGAAAGGAUCAGCAGCCCAGUGACAAGGAUGCCAAGCGAACCAUUUUCGUUGGCAGCCUAAAGUACUGUAAGUAAAG---
(((((.....))))).(((.((((.(((...))).)))).)))..............(((((...(((.((((((.((((.....)))))))))).)))....))))).........--- ( -41.10)
>DroSim_CAF1 12178 117 - 1
GCGGGUGACUCCCGCGUCUAUGGCGGAGAAGUUCAGCCAGGGAAAGGAUCAGCAGCCCAGUGACAAGGAUGCCAAGCGAACCAUUUUCGUUGGCAGCCUAAAGUACUGUAAGUAAAG---
(((((.....))))).(((.((((.(((...))).)))).)))..............(((((...(((.((((((.((((.....)))))))))).)))....))))).........--- ( -38.60)
>DroEre_CAF1 11831 117 - 1
GCGAGUUACUCCCGCGGCCAAGGCGGAAGGUUUUGGCCAAGGAAAGGAUGAACAGCCCAAUGACAAGGAUGCCAAGCGAACCAUUUUCGUGGGCAGCCUAAAAUACUGUAAGUAAUA---
....((((((.((..(((((((((.....)))))))))..)).........((((..........(((.((((..(((((.....))))).)))).)))......)))).)))))).--- ( -34.99)
>DroYak_CAF1 9742 120 - 1
GCGGGUUACUCCCGCGGCUAAGGCGGAGGGUUUUGGCCAGGGAGCGGAUCAGCAGCCCAGUGACAAGGAUGCCAAGCGAACCAUAUUCGUGGGCAGCCUAAAAUACUGUAAGUAUCGUUC
((.((((.(((((..(((((((((.....))))))))).)))))..)))).))....(((((...(((.((((..(((((.....))))).)))).)))....)))))............ ( -44.80)
>consensus
GCGGGUGACUCCCGCGUCUAUGGCGGAGAAGUUCGGCCAGGGAAAGGAUCAGCAGCCCAGUGACAAGGAUGCCAAGCGAACCAUUUUCGUUGGCAGCCUAAAGUACUGUAAGUAAAG___
(((((.....)))))..((.((((.(((...))).)))).))...((........))(((((...(((.(((((.(((((.....)))))))))).)))....)))))............ (-32.20 = -33.04 +   0.84)

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 11:58:30 2006