Locus 2270

Sequence ID 2L_DroMel_CAF1
Location 6,163,352 – 6,163,572
Length 220
Max. P 0.969136
window3641 window3642 window3643 window3644 window3645

overview

Window 1

Location 6,163,352 – 6,163,461
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.09
Mean single sequence MFE -36.73
Consensus MFE -19.29
Energy contribution -20.89
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -2.64
Structure conservation index 0.53
SVM decision value -0.01
SVM RNA-class probability 0.530082
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6163352 109 - 22407834
GGCUAGUGCUGCUGGUGCUUGAGUGUG----------UGCGUAGCCCCCAUUAGCCAA-AGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUCGGUUUUAUUUGAAU
.....((.((((.(((((((..(((((----------(((((............((..-.)).............))))))))))...))))))))))).))((((((......)))))) ( -36.61)
>DroPse_CAF1 11938 112 - 1
UCCGAAUGCUGUGUGUG--------UGUGUGGGUGUUUUCGUGGCCCCCAUUAGCCAAAAGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUUUGUUUUAUGUGAAU
(((...((((.((((((--------(((((.(((((.(((.((((........))))...)))...)))))....)))))))))))...)))).....)))................... ( -33.00)
>DroSim_CAF1 9153 109 - 1
GGCGAGUGCUGCUGGUGCUUGAGUGUG----------UGCGUAGCCCCCAUUAGCCAA-AGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUCGGUUUUAUUUGAAU
..((((((((((.(((((((..(((((----------(((((............((..-.)).............))))))))))...)))))))))))..))))))............. ( -38.01)
>DroYak_CAF1 9186 109 - 1
GGCGAGUGCUGCUGGUGCUUGAGUGUG----------UGCGUAGCCCCCAUUAGCCAA-AGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUCGGUUUUAUUUGAAU
..((((((((((.(((((((..(((((----------(((((............((..-.)).............))))))))))...)))))))))))..))))))............. ( -38.01)
>DroPer_CAF1 11934 120 - 1
UCCGAAUGCUGUGUGUGUGUGAGUGUGUGUGGGUGUUUUCGUGGCCCCCAUUAGCCAAAAGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUUUGUUUUAUGUGAAU
(((...((((.((((((((((..(((((((((((.((((..((((........)))))))).))))))).))))..))))))))))...)))).....)))................... ( -38.00)
>consensus
GGCGAGUGCUGCUGGUGCUUGAGUGUG__________UGCGUAGCCCCCAUUAGCCAA_AGGAUUUAUAUUACAAGCGCACACAUAAAAAGCACCGCAGGAUAUUCGGUUUUAUUUGAAU
.....((.((((.(((((((..(((((..........(((((............((....)).............))))))))))...))))))))))).)).................. (-19.29 = -20.89 +   1.60)

alignment

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secondary structure

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Window 2

Location 6,163,431 – 6,163,534
Length 103
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -33.90
Consensus MFE -26.69
Energy contribution -26.69
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.45
Structure conservation index 0.79
SVM decision value 1.06
SVM RNA-class probability 0.907911
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6163431 103 + 22407834
GCACACACUCAAGCACCAGCAGCACUAGCCAGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCCACUGCAUGCCUCUUGCUCCCAGCUCCC-------GG
((..........)).(((((((........((((((((..(((....)))..)))))))))))))..(((((.....(((.......)))....)))))..-------)) ( -32.10)
>DroSim_CAF1 9232 105 + 1
GCACACACUCAAGCACCAGCAGCACUCGCCAGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCC-----AUGCCUCUUGCUCCCAGCUCCCAGCAACCAG
............((...(((((........((((((((..(((....)))..)))))))))))))..(((((..-----..((.....))....)))))...))...... ( -31.90)
>DroYak_CAF1 9265 105 + 1
GCACACACUCAAGCACCAGCAGCACUCGCCAGAGCUCCCACUGUUCGCAGCAGGAGCUCUCUGCUCCCAGCUCC-----AUGCCUCGUGCUCCGUGCCUUGUGCUCCGAG
((((((((...(((((.(((((........((((((((..(((....)))..)))))))))))))....((...-----..))...)))))..)))...)))))...... ( -37.70)
>consensus
GCACACACUCAAGCACCAGCAGCACUCGCCAGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCC_____AUGCCUCUUGCUCCCAGCUCCC_GC__C_AG
(((........(((...(((((........((((((((..(((....)))..)))))))))))))....)))........))).....((.....))............. (-26.69 = -26.69 +  -0.00)

alignment

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secondary structure

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Window 3

Location 6,163,431 – 6,163,534
Length 103
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 84.62
Mean single sequence MFE -44.70
Consensus MFE -34.90
Energy contribution -35.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.99
Structure conservation index 0.78
SVM decision value 0.44
SVM RNA-class probability 0.736132
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6163431 103 - 22407834
CC-------GGGAGCUGGGAGCAAGAGGCAUGCAGUGGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCUGGCUAGUGCUGCUGGUGCUUGAGUGUGUGC
.(-------(((.((..(.((((...(((.(((((((((((((........))))))).))))))..(((........))))))..)))).)..)).))))......... ( -43.50)
>DroSim_CAF1 9232 105 - 1
CUGGUUGCUGGGAGCUGGGAGCAAGAGGCAU-----GGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCUGGCGAGUGCUGCUGGUGCUUGAGUGUGUGC
....(((((..(((((..(.((.....)).)-----..)))))..)))))((((((((.((((....)))).))))))))..((((..(.....)..))))......... ( -40.90)
>DroYak_CAF1 9265 105 - 1
CUCGGAGCACAAGGCACGGAGCACGAGGCAU-----GGAGCUGGGAGCAGAGAGCUCCUGCUGCGAACAGUGGGAGCUCUGGCGAGUGCUGCUGGUGCUUGAGUGUGUGC
......((((...((((.((((((.((((((-----...((((....)..((((((((..(((....)))..)))))))))))..))))..)).))))))..)))))))) ( -49.70)
>consensus
CU_G__GC_GGGAGCUGGGAGCAAGAGGCAU_____GGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCUGGCGAGUGCUGCUGGUGCUUGAGUGUGUGC
.............((.....(((..((((((.....(.(((.(...((..((((((((..(((....)))..)))))))).))..).))).)..))))))...)))..)) (-34.90 = -35.23 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,163,461 – 6,163,572
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.57
Mean single sequence MFE -39.33
Consensus MFE -30.08
Energy contribution -30.75
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.76
SVM decision value 1.64
SVM RNA-class probability 0.969136
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6163461 111 + 22407834
AGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCCACUGCAUGCCUCUUGCUCCCAGCUCCC-------GGUUCCAUGC--UUCCGAAAAACGUGGAAAAAGAGCAAUGAA
((((((((..(((....)))..)))))))).(((((.(((((.....(((.......)))....)))))..-------..(((((((.--..........)))))))...)))))..... ( -39.30)
>DroSim_CAF1 9262 113 + 1
AGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCC-----AUGCCUCUUGCUCCCAGCUCCCAGCAACCAGUUCCAUGC--UCCCGAAAAACGUGGAAAAAGAGCAAUGAA
((((((((..(((....)))..)))))))).(((((.(((((..-----..((.....))....)))))...........(((((((.--..........)))))))...)))))..... ( -37.80)
>DroYak_CAF1 9295 115 + 1
AGAGCUCCCACUGUUCGCAGCAGGAGCUCUCUGCUCCCAGCUCC-----AUGCCUCGUGCUCCGUGCCUUGUGCUCCGAGCUCCAUGCCAUCCCGAAAAACGGGGAAAAAGAGCAAUGAA
((((((((..(((....)))..)))))))).(((((..(((((.-----..(((..(.((.....)))..).))...)))))........(((((.....))))).....)))))..... ( -40.90)
>consensus
AGAGCUCCAACUGUUCGCAGCAGGAGCUCUCUGCUCCGAGCUCC_____AUGCCUCUUGCUCCCAGCUCCC_GC__C_AGUUCCAUGC__UCCCGAAAAACGUGGAAAAAGAGCAAUGAA
((((((((..(((....)))..)))))))).(((((.((((.................))))...................((((((.............))))))....)))))..... (-30.08 = -30.75 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,163,461 – 6,163,572
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -46.70
Consensus MFE -34.55
Energy contribution -34.33
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.34
Structure conservation index 0.74
SVM decision value 0.92
SVM RNA-class probability 0.882684
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6163461 111 - 22407834
UUCAUUGCUCUUUUUCCACGUUUUUCGGAA--GCAUGGAACC-------GGGAGCUGGGAGCAAGAGGCAUGCAGUGGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCU
....((((((...(((((.(((((...)))--)).))))).(-------(((.((((.(.((.....)).).))))....))))))))))((((((((.((((....)))).)))))))) ( -45.10)
>DroSim_CAF1 9262 113 - 1
UUCAUUGCUCUUUUUCCACGUUUUUCGGGA--GCAUGGAACUGGUUGCUGGGAGCUGGGAGCAAGAGGCAU-----GGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCU
....(((((((..(((((.((((.....))--)).)))))(..(((......)))..)((((.........-----...)))))))))))((((((((.((((....)))).)))))))) ( -43.00)
>DroYak_CAF1 9295 115 - 1
UUCAUUGCUCUUUUUCCCCGUUUUUCGGGAUGGCAUGGAGCUCGGAGCACAAGGCACGGAGCACGAGGCAU-----GGAGCUGGGAGCAGAGAGCUCCUGCUGCGAACAGUGGGAGCUCU
....((((((((.(((((((.....))).(((.(.((..((((.(.((.....)).).)))).)).).)))-----))))..))))))))((((((((..(((....)))..)))))))) ( -52.00)
>consensus
UUCAUUGCUCUUUUUCCACGUUUUUCGGGA__GCAUGGAACU_G__GC_GGGAGCUGGGAGCAAGAGGCAU_____GGAGCUCGGAGCAGAGAGCUCCUGCUGCGAACAGUUGGAGCUCU
....(((((((..((((..(((((...(.....)..)))))............((.....))..............))))...)))))))((((((((..(((....)))..)))))))) (-34.55 = -34.33 +  -0.22)

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 10:23:39 2006