Locus 2615

Sequence ID 2R_DroMel_CAF1
Location 9,213,523 – 9,213,666
Length 143
Max. P 0.995028
window4310 window4311 window4312 window4313

overview

Window 0

Location 9,213,523 – 9,213,631
Length 108
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 85.40
Mean single sequence MFE -27.73
Consensus MFE -19.88
Energy contribution -20.80
Covariance contribution 0.92
Combinations/Pair 1.10
Mean z-score -2.50
Structure conservation index 0.72
SVM decision value 0.05
SVM RNA-class probability 0.560936
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9213523 108 + 20766785
UUUGUCGAGCACCUACUUUUCGGUGCUGCUCGGCUCUAGCACUCACCUUUCCGGUAAUUUGUGCAU-UUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU-
...((((((((.(.(((....)))).))))))))....((....(((.....)))...((((((..-....))))))......))........((((.....))))...- ( -28.90)
>DroSec_CAF1 107146 108 + 1
UUUGUCGAGCACCUACUUUUCGGUGCUGCUCGGCUCCAGCACUCACCUUGCCGGUAAUUUGUGCAU-UUUCGCAUAAUAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU-
...((((((((.(.(((....)))).))))))))...............(((((.((.((((((..-................)))))).)).))((.....)))))..- ( -29.47)
>DroSim_CAF1 90185 108 + 1
UUUGUCGAGCACCUACUUUUCGGUGCUGCUCGGCUCCAGCACUCACCUUGCCGGUAAUUUGUGCAU-UUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU-
...((((((((.(.(((....)))).))))))))...............(((((.((.((((((..-................)))))).)).))((.....)))))..- ( -29.47)
>DroEre_CAF1 93035 108 + 1
UUUGUCGAGCACCUACUUUUCGGUGCUACUCGGCGCCAGCACUCACCUUGCCGGUAAUUUGUGCAU-UUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU-
...((((((((((........)))))...)))))(((.(((.......(((.((.((.((((((..-................)))))).)).)))))...))))))..- ( -31.77)
>DroYak_CAF1 89465 108 + 1
UUUGUCGAGCACCUACUUUUCGGUGCUACUCGGCUCCAGCACUCACCUUGCCGGUAAUUUGUGCAU-UUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU-
...((((((((((........)))))...)))))...............(((((.((.((((((..-................)))))).)).))((.....)))))..- ( -28.97)
>DroPer_CAF1 76913 90 + 1
UUUCUCCAG------GCUUUCGACGCUCCUCGA------CACUCACCUUGAAUGUAAUUUGUGCACAUUUCUCGACAGAUU--------UUUGCCACAUUUUGUGGCCUG
......(((------((..((((......))))------....(((...((((((.....(.(((.(..(((....)))..--------).)))))))))).)))))))) ( -17.80)
>consensus
UUUGUCGAGCACCUACUUUUCGGUGCUGCUCGGCUCCAGCACUCACCUUGCCGGUAAUUUGUGCAU_UUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUU_
...((((((((((........))))))...))))....((((..(((.....))).....)))).............................((((.....)))).... (-19.88 = -20.80 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,213,523 – 9,213,631
Length 108
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 85.40
Mean single sequence MFE -30.31
Consensus MFE -21.75
Energy contribution -22.58
Covariance contribution 0.84
Combinations/Pair 1.09
Mean z-score -2.60
Structure conservation index 0.72
SVM decision value 0.11
SVM RNA-class probability 0.590114
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9213523 108 - 20766785
-AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAA-AUGCACAAAUUACCGGAAAGGUGAGUGCUAGAGCCGAGCAGCACCGAAAAGUAGGUGCUCGACAAA
-...((((.....))))....((((......((((..((....-..((((...(((((.....)))))))))....))..))))(((((........)))))...)))). ( -31.30)
>DroSec_CAF1 107146 108 - 1
-AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUAUUAUGCGAAA-AUGCACAAAUUACCGGCAAGGUGAGUGCUGGAGCCGAGCAGCACCGAAAAGUAGGUGCUCGACAAA
-...((((.....))))....((((((................-..))))))....((((((.......)))))).(.((((((.(((......)).).)))))).)... ( -32.07)
>DroSim_CAF1 90185 108 - 1
-AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAA-AUGCACAAAUUACCGGCAAGGUGAGUGCUGGAGCCGAGCAGCACCGAAAAGUAGGUGCUCGACAAA
-...((((.....))))....((((((....((.....))...-..))))))....((((((.......)))))).(.((((((.(((......)).).)))))).)... ( -32.30)
>DroEre_CAF1 93035 108 - 1
-AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAA-AUGCACAAAUUACCGGCAAGGUGAGUGCUGGCGCCGAGUAGCACCGAAAAGUAGGUGCUCGACAAA
-...((((.....))))....((((((....((.....))...-..))))))..(((((((..(((....)))...)))).)))(((((........)))))........ ( -32.40)
>DroYak_CAF1 89465 108 - 1
-AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAA-AUGCACAAAUUACCGGCAAGGUGAGUGCUGGAGCCGAGUAGCACCGAAAAGUAGGUGCUCGACAAA
-...((((.....))))....((((((....((.....))...-..))))))..(((((((..(((....)))...)))).)))(((((........)))))........ ( -32.40)
>DroPer_CAF1 76913 90 - 1
CAGGCCACAAAAUGUGGCAAA--------AAUCUGUCGAGAAAUGUGCACAAAUUACAUUCAAGGUGAGUG------UCGAGGAGCGUCGAAAGC------CUGGAGAAA
(((((((((.....(((((..--------....))))).....)))).........(((((.....)))))------((((......))))..))------)))...... ( -21.40)
>consensus
_AAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAA_AUGCACAAAUUACCGGCAAGGUGAGUGCUGGAGCCGAGCAGCACCGAAAAGUAGGUGCUCGACAAA
....((((.....))))..............((((...........((((...(((((.....)))))))))...........((((((........)))))).)))).. (-21.75 = -22.58 +   0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,213,559 – 9,213,666
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 95.51
Mean single sequence MFE -32.76
Consensus MFE -27.03
Energy contribution -27.27
Covariance contribution 0.24
Combinations/Pair 1.10
Mean z-score -1.63
Structure conservation index 0.83
SVM decision value 0.53
SVM RNA-class probability 0.770973
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9213559 107 + 20766785
UAGCACUCACCUUUCCGGUAAUUUGUGCAUUUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGUGAGGAAUGCUGUGGGAUGCUGC
((((((((((..((((......((((((......))))))(((((.((((......((((.....))))......))).).))))).))))....))))).))))). ( -33.30)
>DroSec_CAF1 107182 107 + 1
CAGCACUCACCUUGCCGGUAAUUUGUGCAUUUUCGCAUAAUAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGUGAGGAAUGCUGUGGGAUGCUGA
((((((((((...((.(.(((.((((((......))))))...))).)......((((.(((((((..((.....))..))))))).)))).)).))))).))))). ( -34.60)
>DroSim_CAF1 90221 107 + 1
CAGCACUCACCUUGCCGGUAAUUUGUGCAUUUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGUGAGGAAUGCUGUGGGAUGCUGC
((((((((((...((.(.(((.((((((......))))))...))).)......((((.(((((((..((.....))..))))))).)))).)).))))).))))). ( -33.20)
>DroEre_CAF1 93071 107 + 1
CAGCACUCACCUUGCCGGUAAUUUGUGCAUUUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGCCAGGAAUCCUGCGGAAUGCUGG
(((((.......(((..(....((((((......))))))...)..))).....(((((((..((.(((((..(.....)..)))).).))...)))))))))))). ( -31.80)
>DroYak_CAF1 89501 107 + 1
CAGCACUCACCUUGCCGGUAAUUUGUGCAUUUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGCGAAGAAUGCUGUGGCAUGCUGC
(((((.......(((((.....((((((......))))))....(((((.......((((.....))))(((((..(....)..)))))..))))))))))))))). ( -30.91)
>consensus
CAGCACUCACCUUGCCGGUAAUUUGUGCAUUUUCGCAUAACAUUUAGCACAAUUUUCCGCAUUUUGCGGCUUCGAGUGACAGAGUGAGGAAUGCUGUGGGAUGCUGC
((((((((((......((.((.((((((..................)))))).)).))(((((((...(((..(.....)..)))..))))))).))))).))))). (-27.03 = -27.27 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,213,559 – 9,213,666
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 95.51
Mean single sequence MFE -31.45
Consensus MFE -27.95
Energy contribution -28.35
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -2.05
Structure conservation index 0.89
SVM decision value 2.53
SVM RNA-class probability 0.995028
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9213559 107 - 20766785
GCAGCAUCCCACAGCAUUCCUCACUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAAAUGCACAAAUUACCGGAAAGGUGAGUGCUA
............(((((((.((..((((..........((((.....))))....((((((....((.....)).....)))))).....))))..)).))))))). ( -26.20)
>DroSec_CAF1 107182 107 - 1
UCAGCAUCCCACAGCAUUCCUCACUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUAUUAUGCGAAAAUGCACAAAUUACCGGCAAGGUGAGUGCUG
...........(((((...(((((..((((........((((.....))))....((((((..................))))))......))))..)))))))))) ( -32.37)
>DroSim_CAF1 90221 107 - 1
GCAGCAUCCCACAGCAUUCCUCACUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAAAUGCACAAAUUACCGGCAAGGUGAGUGCUG
...........(((((...(((((..((((........((((.....))))....((((((....((.....)).....))))))......))))..)))))))))) ( -32.60)
>DroEre_CAF1 93071 107 - 1
CCAGCAUUCCGCAGGAUUCCUGGCUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAAAUGCACAAAUUACCGGCAAGGUGAGUGCUG
.((((((((..((((...))))((..((((........((((.....))))....((((((....((.....)).....))))))......))))..)))))))))) ( -34.30)
>DroYak_CAF1 89501 107 - 1
GCAGCAUGCCACAGCAUUCUUCGCUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAAAUGCACAAAUUACCGGCAAGGUGAGUGCUG
.((((((((....)).....((((..((((........((((.....))))....((((((....((.....)).....))))))......))))..)))))))))) ( -31.80)
>consensus
GCAGCAUCCCACAGCAUUCCUCACUCUGUCACUCGAAGCCGCAAAAUGCGGAAAAUUGUGCUAAAUGUUAUGCGAAAAUGCACAAAUUACCGGCAAGGUGAGUGCUG
...........(((((...(((((..((((........((((.....))))....((((((..................))))))......))))..)))))))))) (-27.95 = -28.35 +   0.40)

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 10:34:37 2006