Locus 6509

Sequence ID 3L_DroMel_CAF1
Location 17,264,975 – 17,265,195
Length 220
Max. P 0.999333
window10530 window10531 window10532 window10533 window10534

overview

Window 0

Location 17,264,975 – 17,265,095
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.58
Mean single sequence MFE -30.80
Consensus MFE -28.88
Energy contribution -28.84
Covariance contribution -0.04
Combinations/Pair 1.10
Mean z-score -2.10
Structure conservation index 0.94
SVM decision value 2.89
SVM RNA-class probability 0.997618
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17264975 120 - 23771897
AACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...(((((((.((((((.......))))))..(.......)...)))))))(((.((((((..(..(((((..........)))))..).(....))))))))))............... ( -31.90)
>DroSec_CAF1 148489 120 - 1
AACCGAACGAAUGCCUCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...(((((((..((..........))(((....)))........)))))))(((.((((((..(..(((((..........)))))..).(....))))))))))............... ( -27.30)
>DroSim_CAF1 143523 120 - 1
AACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...(((((((.((((((.......))))))..(.......)...)))))))(((.((((((..(..(((((..........)))))..).(....))))))))))............... ( -31.90)
>DroEre_CAF1 151542 119 - 1
AACCGAACGAAUGCCG-CCCAAUAGCGGCAAAGGCGAAAACAAAUCGUUUGUGCCCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...........(((((-((.....(.((((.((((((.......)))))).)))))(((.((.(..(((((..........)))))..).))...))))))))))............... ( -34.00)
>DroYak_CAF1 156007 120 - 1
AACCGAACGAAUGUCGUCCCAAUAGCGGCGAAGGCGAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...........(((((((.(....(((((((..(((.((((.....)))).))))))))))..(..(((((..........)))))..).......).)))))))............... ( -28.90)
>consensus
AACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUUAAAAUGAACAUGAAAAGCGGCGGCAGAUAAAGAGCAAAUG
...(((((((.((((((.......))))))..(.......)...)))))))(((.((((((..(..(((((..........)))))..).(....))))))))))............... (-28.88 = -28.84 +  -0.04)

alignment

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secondary structure

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Window 1

Location 17,265,015 – 17,265,135
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.25
Mean single sequence MFE -33.08
Consensus MFE -29.28
Energy contribution -29.44
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -2.21
Structure conservation index 0.89
SVM decision value 2.44
SVM RNA-class probability 0.993959
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17265015 120 - 23771897
GUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUU
(((......................((....))(((((.....).......((((((.......))))))..))))....(((((.(((..(((.....)))..)))))))))))..... ( -34.20)
>DroSec_CAF1 148529 120 - 1
GUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCUCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUU
(((((...................(((....))).((......(((((((..((..........))(((....)))........)))))))(((.....))).)).....)))))..... ( -29.00)
>DroSim_CAF1 143563 120 - 1
GUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUU
(((......................((....))(((((.....).......((((((.......))))))..))))....(((((.(((..(((.....)))..)))))))))))..... ( -34.20)
>DroEre_CAF1 151582 119 - 1
GUCUAUUUCAUUAAUACAAAUAAAGCCGGAAGGGGCCGAAAACCGAACGAAUGCCG-CCCAAUAGCGGCAAAGGCGAAAACAAAUCGUUUGUGCCCGCUGCAAGGACAUUUGGACAAAUU
(((..((((................((....)).((((.....).......(((((-(......))))))..))))))).(((((.(((..(((.....)))..)))))))))))..... ( -32.70)
>DroYak_CAF1 156047 120 - 1
GUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGUCGUCCCAAUAGCGGCGAAGGCGAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUU
(((((.(((...............(((....)))..((.....))...)))....((((...((((((((.((((((.......)))))).))).)))))...))))...)))))..... ( -35.30)
>consensus
GUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAACAAAUCGUUUGUGCUCGCUGCAAGGACAUUUGGACAAAUU
(((.....................(((....)))((((.....).......((((((.......))))))..))).....(((((.(((..(((.....)))..)))))))))))..... (-29.28 = -29.44 +   0.16)

alignment

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secondary structure

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Window 2

Location 17,265,055 – 17,265,174
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.90
Mean single sequence MFE -30.70
Consensus MFE -27.58
Energy contribution -27.74
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -2.67
Structure conservation index 0.90
SVM decision value 3.52
SVM RNA-class probability 0.999333
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17265055 119 - 23771897
GGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAA
((((((((((......(((........))).....-.)))))))....................(((....)))))).......(..(...((((((.......))))))..)..).... ( -32.80)
>DroSec_CAF1 148569 120 - 1
GGCAGACGUUGAAAAAUCACUUUAGCAUGAACCCAAAAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCUCCCCAAUAGCGGCAAAGGCCAAAA
((((((((((......(((........))).......)))))))....................(((....))))))...............((((..((......))...))))..... ( -27.62)
>DroSim_CAF1 143603 119 - 1
GGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAA
((((((((((......(((........))).....-.)))))))....................(((....)))))).......(..(...((((((.......))))))..)..).... ( -32.80)
>DroEre_CAF1 151622 118 - 1
GGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAAGCCGGAAGGGGCCGAAAACCGAACGAAUGCCG-CCCAAUAGCGGCAAAGGCGAAAA
((((((((((......(((........))).....-.))))))).....................((....)).)))..........((..(((((-(......))))))....)).... ( -30.20)
>DroYak_CAF1 156087 119 - 1
GGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGUCGUCCCAAUAGCGGCGAAGGCGAAAA
.(((((((((......(((........))).....-.))))))).((((...............(((....)))((((........(((.....)))........))))))))))..... ( -30.09)
>consensus
GGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA_AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAAAACCGAACGAAUGCCGCCCCAAUAGCGGCAAAGGCCAAAA
((((((((((......(((........))).......)))))))....................(((....))))))..............((((((.......)))))).......... (-27.58 = -27.74 +   0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,265,095 – 17,265,195
Length 100
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 88.43
Mean single sequence MFE -32.12
Consensus MFE -26.65
Energy contribution -26.28
Covariance contribution -0.37
Combinations/Pair 1.10
Mean z-score -1.99
Structure conservation index 0.83
SVM decision value 1.01
SVM RNA-class probability 0.899945
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17265095 100 + 23771897
UUCGGCCCCUUCCGGGUUUAUUUGUAUUAAUGAAAUAGACGUUU-UGGGGUCAUGCUAAAGUGAUUUUUCAACGUCUGCCA------------GAAGCAGCCGGGUGGUGUGG
((((((..((((.((.((((((......)))))).((((((((.-.((((((((......))))))))..)))))))))).------------))))..))))))........ ( -32.30)
>DroSec_CAF1 148609 97 + 1
UUCGGCCCCUUCCGGGUUUAUUUGUAUUAAUGAAAUAGACGUUUUUGGGUUCAUGCUAAAGUGAUUUUUCAACGUCUGCCA------------GAAGCAGCCGAGUGGU----
((((((..((((.((.((((((......)))))).((((((((...(((.((((......)))).)))..)))))))))).------------))))..))))))....---- ( -28.60)
>DroSim_CAF1 143643 96 + 1
UUCGGCCCCUUCCGGGUUUAUUUGUAUUAAUGAAAUAGACGUUU-UGGGGUCAUGCUAAAGUGAUUUUUCAACGUCUGCCA------------GAAGCAGCCGAGUGGU----
((((((..((((.((.((((((......)))))).((((((((.-.((((((((......))))))))..)))))))))).------------))))..))))))....---- ( -33.30)
>DroYak_CAF1 156127 110 + 1
UUCGGCCCCUUCCGGGUUUAUUUGUAUUAAUGAAAUAGACGUUU-UGGGGUCAUGCUAAAGUGAUUUUUCAACGUCUGCCACAAGCAGGGGCAGAAGCAGUUGGCUGGAGG--
(((.((((((.(..((((((((......)))))).((((((((.-.((((((((......))))))))..))))))))))....).)))))).))).(((....)))....-- ( -34.30)
>consensus
UUCGGCCCCUUCCGGGUUUAUUUGUAUUAAUGAAAUAGACGUUU_UGGGGUCAUGCUAAAGUGAUUUUUCAACGUCUGCCA____________GAAGCAGCCGAGUGGU____
.(((((..((((....((((((......)))))).((((((((...((((((((......))))))))..))))))))...............))))..)))))......... (-26.65 = -26.28 +  -0.37)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,265,095 – 17,265,195
Length 100
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 88.43
Mean single sequence MFE -28.05
Consensus MFE -21.67
Energy contribution -21.67
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.25
Structure conservation index 0.77
SVM decision value 1.82
SVM RNA-class probability 0.978853
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17265095 100 - 23771897
CCACACCACCCGGCUGCUUC------------UGGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAA
..........(((((.((((------------(((.(((((((......(((........))).....-.)))))))(((.....)))..........))))))).))))).. ( -28.20)
>DroSec_CAF1 148609 97 - 1
----ACCACUCGGCUGCUUC------------UGGCAGACGUUGAAAAAUCACUUUAGCAUGAACCCAAAAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAA
----.....((((((.((((------------(((.(((((((......(((........))).......)))))))(((.....)))..........))))))).)))))). ( -29.02)
>DroSim_CAF1 143643 96 - 1
----ACCACUCGGCUGCUUC------------UGGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAA
----.....((((((.((((------------(((.(((((((......(((........))).....-.)))))))(((.....)))..........))))))).)))))). ( -29.60)
>DroYak_CAF1 156127 110 - 1
--CCUCCAGCCAACUGCUUCUGCCCCUGCUUGUGGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA-AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAA
--......((((...((..........))...))))(((((((......(((........))).....-.)))))))....................(((....)))...... ( -25.40)
>consensus
____ACCACCCGGCUGCUUC____________UGGCAGACGUUGAAAAAUCACUUUAGCAUGACCCCA_AAACGUCUAUUUCAUUAAUACAAAUAAACCCGGAAGGGGCCGAA
................................(((((((((((......(((........))).......)))))))....................(((....))))))).. (-21.67 = -21.67 +  -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 12:22:02 2006