Locus 6076

Sequence ID 2L_DroMel_CAF1
Location 17,071,896 – 17,072,054
Length 158
Max. P 0.972078
window9665 window9666 window9667

overview

Window 5

Location 17,071,896 – 17,072,016
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.21
Mean single sequence MFE -29.05
Consensus MFE -15.94
Energy contribution -17.90
Covariance contribution 1.96
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.55
SVM decision value 0.21
SVM RNA-class probability 0.634857
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17071896 120 + 22407834
AAAAAGGCAAAAGCCAAGUGACACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACUUCUGGGUGUUGCCACAAGCGGAAAAGCUGGUAGUGGGCAG
............(((..(..(((((((((.(.((...(((((((....(((......)))....)))).)))..))).)))))..))))..)(((.(((......)))....)))))).. ( -32.30)
>DroPse_CAF1 23238 101 + 1
AAA-----------AAAGUGCCACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACCUGGGGGAG--------GGCUGGGGUGUGGGGUGUGGGCAG
...-----------....((((...((.((....))............(((......))).))....((..(..(((((((.((....--------..)).)))))))..)..)))))). ( -28.90)
>DroSec_CAF1 35856 120 + 1
AAAAAGGCAAAAGCCAAGUGACACAGAAGCGACGGCAACAAAUGAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACUUCUGGGUGUUGCCACAAGCGGAAAAGCUGGUAGUGGGCAG
............(((..(..(((((((((.(.((...((((((.....(((......))).....))).)))..))).)))))..))))..)(((.(((......)))....)))))).. ( -32.30)
>DroEre_CAF1 35293 119 + 1
AAAAAGGCAAAAGCCAAGUGACACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACUUCUGGGUGUUGCCACAAGGGG-AAAGCUGGUAGUGGGCGG
............(((..(..(((((((((.(.((...(((((((....(((......)))....)))).)))..))).)))))..))))..)(((..((..-....))....)))))).. ( -28.40)
>DroYak_CAF1 35562 115 + 1
AAAAAGGCAAAAGCCAAGUGACACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACUUCUGGGUGUUGCCACAAGG-----AGCUGCUACUGGAAGG
.....(((....)))..(((.((((...((....))............(((......))).........)))).))).((((..(..((.((.......-----.)).))..)..)))). ( -29.00)
>DroPer_CAF1 21190 93 + 1
AAA-----------AAAGUGCCACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACCUGGGGA-G--------GG-------GUGGGGUGUGGGCAG
...-----------....(((((((...((....))............(((......))).........)))..(((((((.(...-.--------..-------.).))))))))))). ( -23.40)
>consensus
AAAAAGGCAAAAGCCAAGUGACACAGAAGCGACGGCAACAAAUUAAAAGCCAUAAAAGGCAUCAAAUUAUGUGACGCACUUCUGGGUGUUGCCACAAGCGG_AAAGCUGGUAGUGGGCAG
.....(((((.(.(((((((.((((...((....))............(((......))).........))))...))))..))).).)))))........................... (-15.94 = -17.90 +   1.96)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,071,896 – 17,072,016
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.21
Mean single sequence MFE -29.35
Consensus MFE -19.18
Energy contribution -20.10
Covariance contribution 0.92
Combinations/Pair 1.11
Mean z-score -2.95
Structure conservation index 0.65
SVM decision value 1.50
SVM RNA-class probability 0.959232
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17071896 120 - 22407834
CUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGUCACUUGGCUUUUGCCUUUUU
.((((.((....(((......))).))))))..((.((((((((((.((.((((.((((.(((......)))..)))).)))))).)).)))))))).)).....(((....)))..... ( -34.70)
>DroPse_CAF1 23238 101 - 1
CUGCCCACACCCCACACCCCAGCC--------CUCCCCCAGGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGGCACUUU-----------UUU
...........(((((....(((.--------.......(((.((((((.......)))))))))..(((((............))))).)))..)))))......-----------... ( -19.70)
>DroSec_CAF1 35856 120 - 1
CUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUCAUUUGUUGCCGUCGCUUCUGUGUCACUUGGCUUUUGCCUUUUU
.((((.((....(((......))).))))))..((.((((((((((.((.((((..(((.(((......)))...))).)))))).)).)))))))).)).....(((....)))..... ( -34.50)
>DroEre_CAF1 35293 119 - 1
CCGCCCACUACCAGCUUU-CCCCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGUCACUUGGCUUUUGCCUUUUU
.............((...-..((..((((((.....((((((((((.((.((((.((((.(((......)))..)))).)))))).)).))))))))))))))..)).....))...... ( -33.10)
>DroYak_CAF1 35562 115 - 1
CCUUCCAGUAGCAGCU-----CCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGUCACUUGGCUUUUGCCUUUUU
.......((((.((((-----....((((((.....((((((((((.((.((((.((((.(((......)))..)))).)))))).)).))))))))))))))..)))).))))...... ( -34.80)
>DroPer_CAF1 21190 93 - 1
CUGCCCACACCCCAC-------CC--------C-UCCCCAGGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGGCACUUU-----------UUU
.((((.(((....((-------(.--------.-......)))(((.(.(((((.((((.(((......)))..)))).))).))..).)))...)))))))....-----------... ( -19.30)
>consensus
CUGCCCACUACCAGCUUU_CCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUUUGUUGCCGUCGCUUCUGUGUCACUUGGCUUUUGCCUUUUU
.................................((.((((((((((.((.((((.((((.(((......)))..)))).)))))).)).)))))))).)).....(((....)))..... (-19.18 = -20.10 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,071,936 – 17,072,054
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.24
Mean single sequence MFE -20.28
Consensus MFE -14.29
Energy contribution -15.02
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -1.76
Structure conservation index 0.70
SVM decision value 1.69
SVM RNA-class probability 0.972078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17071936 118 - 22407834
-CCCUUCUCCACCUUCCGACCUCCACUCCACCACCCAU-UCUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
-.....................................-...(((..((((.(((......))).))))........(((((.((((((.......)))))))))))..)))........ ( -20.60)
>DroPse_CAF1 23267 106 - 1
CUCCUUCUG---UUUGUGGC-UGGAAACA-CCCCUCCC-CCUGCCCACACCCCACACCCCAGCC--------CUCCCCCAGGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
.........---..((((((-((....))-........-......................(((--------((.....))).))))))))....((((.(((......)))..)))).. ( -19.10)
>DroSec_CAF1 35896 115 - 1
-CCCUGCCCCUCCUCACGACCAGCACUCC---ACCCAU-UCUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUCAUU
-................(((..(((((..---......-((((.........(((......))).(((....))).))))))))))))........(((.(((......)))...))).. ( -22.50)
>DroSim_CAF1 31191 118 - 1
-CCCUGCCCCUCCUCACGACCAGCACUCCACCACCCAU-UCUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
-....(((..............................-..((((.((....(((......))).))))))......(((((.((((((.......)))))))))))..)))........ ( -21.90)
>DroEre_CAF1 35333 107 - 1
--CGCGCCCC--CACCCCAUCAGC-CCCU------CAC-UCCGCCCACUACCAGCUUU-CCCCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
--........--.........(((-(...------...-...................-......(((....)))..(((((.((((((.......)))))))))))..))))....... ( -19.20)
>DroYak_CAF1 35602 109 - 1
-UCGUGCCCCUUUACCCCAUCAAC-CACCAC----CACCCCCUUCCAGUAGCAGCU-----CCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
-....(((................-......----.....................-----....(((....)))..(((((.((((((.......)))))))))))..)))........ ( -18.40)
>consensus
_CCCUGCCCCUCCUCCCGACCAGCACUCC_C_ACCCAC_UCUGCCCACUACCAGCUUUUCCGCUUGUGGCAACACCCAGAAGUGCGUCACAUAAUUUGAUGCCUUUUAUGGCUUUUAAUU
..........................................(((....................(((....)))..(((((.((((((.......)))))))))))..)))........ (-14.29 = -15.02 +   0.72)

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 12:00:45 2006