Locus 3236

Sequence ID 2R_DroMel_CAF1
Location 11,056,225 – 11,056,358
Length 133
Max. P 0.882946
window5316 window5317 window5318 window5319

overview

Window 6

Location 11,056,225 – 11,056,322
Length 97
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 83.75
Mean single sequence MFE -30.27
Consensus MFE -21.60
Energy contribution -21.58
Covariance contribution -0.02
Combinations/Pair 1.36
Mean z-score -3.19
Structure conservation index 0.71
SVM decision value 0.82
SVM RNA-class probability 0.858705
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11056225 97 + 20766785
UA-AGCGCACUACCCAGCACCAACUGGUUAUCG-AUUGGCUACGGGCAGUAGCCAACACUGUCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCU
..-((.(((((....(((.((((((((.....(-.((((((((.....)))))))))..((.(....).))....)))))))).)))....))))).)) ( -32.00)
>DroVir_CAF1 3350 89 + 1
UGU-GUGUGUUUUGCAGCACUU------UAUCUAAGUUACUG-UGGCCUUAACCAACACUGUAUUUAUCCA--GUCCAGUUGGAGUUUUUCAGUGUUCU
.(.-((.....(..(((.((((------.....))))..)))-..).....)))(((((((......((((--(.....)))))......))))))).. ( -18.90)
>DroSec_CAF1 3045 97 + 1
UA-AGCGCACUACCCAGCACCAACUGGUUAUCG-AUUGGCUACGGGCAGUAGCCAACACUGUCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUGCU
..-((((((((....(((.((((((((.....(-.((((((((.....)))))))))..((.(....).))....)))))))).)))....)))))))) ( -37.90)
>DroSim_CAF1 2392 97 + 1
UA-AGCGCACUACCCAGCACCAACUGGUUAUCG-AUUGGCUACGGGCAGUAGCCAACACUGUCAUCCGUCAUUUUCCAGUAGGAGUUUUUCAGUGUUCU
..-((.(((((....(((.((.(((((.....(-.((((((((.....)))))))))..((.(....).))....))))).)).)))....))))).)) ( -27.90)
>DroEre_CAF1 3052 97 + 1
UC-AACACACUUCCCAGCACCAACUGGUUAUCG-AUUGGCUACUGGCAGUAGCCAACACUGCCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCU
..-...(((((....(((.((((((((....((-..((((...((((....)))).....))))..)).......)))))))).)))....)))))... ( -32.70)
>DroYak_CAF1 3055 97 + 1
UC-AUCACACUUCCCAGCACCAACUGGUUAUCG-AUUGGCUACGGGCAGUAGCCAACACUGCCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCU
..-...(((((....(((.((((((((....((-..((((....(((....)))......))))..)).......)))))))).)))....)))))... ( -32.20)
>consensus
UA_AGCGCACUACCCAGCACCAACUGGUUAUCG_AUUGGCUACGGGCAGUAGCCAACACUGUCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCU
......(((((....(((.((((((((....((...((((....(((....)))......))))..)).......)))))))).)))....)))))... (-21.60 = -21.58 +  -0.02)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,056,225 – 11,056,322
Length 97
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 83.75
Mean single sequence MFE -30.60
Consensus MFE -18.87
Energy contribution -19.82
Covariance contribution 0.95
Combinations/Pair 1.14
Mean z-score -2.68
Structure conservation index 0.62
SVM decision value 0.11
SVM RNA-class probability 0.589027
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11056225 97 - 20766785
AGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGACAGUGUUGGCUACUGCCCGUAGCCAAU-CGAUAACCAGUUGGUGCUGGGUAGUGCGCU-UA
((..(((((.......((((((((......((........))(((((((((.....)))))))))-......)))))))).......)))))..))-.. ( -32.14)
>DroVir_CAF1 3350 89 - 1
AGAACACUGAAAAACUCCAACUGGAC--UGGAUAAAUACAGUGUUGGUUAAGGCCA-CAGUAACUUAGAUA------AAGUGCUGCAAAACACAC-ACA
..(((((((......((((.......--))))......)))))))(((....))).-(((((.(((.....------))))))))..........-... ( -18.60)
>DroSec_CAF1 3045 97 - 1
AGCACACUGAAAAACUCCAACUGGAAAAUGACGGAUGACAGUGUUGGCUACUGCCCGUAGCCAAU-CGAUAACCAGUUGGUGCUGGGUAGUGCGCU-UA
(((.(((((.......((((((((......((........))(((((((((.....)))))))))-......)))))))).......))))).)))-.. ( -35.84)
>DroSim_CAF1 2392 97 - 1
AGAACACUGAAAAACUCCUACUGGAAAAUGACGGAUGACAGUGUUGGCUACUGCCCGUAGCCAAU-CGAUAACCAGUUGGUGCUGGGUAGUGCGCU-UA
..(((((((......(((....)))......(....).)))))))((((((((((((..((((((-.(.....).))))))..))))))))).)))-.. ( -31.80)
>DroEre_CAF1 3052 97 - 1
AGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGGCAGUGUUGGCUACUGCCAGUAGCCAAU-CGAUAACCAGUUGGUGCUGGGAAGUGUGUU-GA
...(((((........((((((((....(((.((.((((((((.....))))))))....))..)-))....))))))))........)))))...-.. ( -33.29)
>DroYak_CAF1 3055 97 - 1
AGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGGCAGUGUUGGCUACUGCCCGUAGCCAAU-CGAUAACCAGUUGGUGCUGGGAAGUGUGAU-GA
...(((((.....((((((.(((........))).))).)))(((((((((.....)))))))))-......(((((....)))))..)))))...-.. ( -31.90)
>consensus
AGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGACAGUGUUGGCUACUGCCCGUAGCCAAU_CGAUAACCAGUUGGUGCUGGGAAGUGCGCU_UA
..(((((((......(((....)))......(....).)))))))((((((.....))))))..........(((((....)))))............. (-18.87 = -19.82 +   0.95)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,056,246 – 11,056,358
Length 112
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 74.93
Mean single sequence MFE -32.19
Consensus MFE -13.31
Energy contribution -12.39
Covariance contribution -0.91
Combinations/Pair 1.40
Mean z-score -1.96
Structure conservation index 0.41
SVM decision value 0.05
SVM RNA-class probability 0.559616
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11056246 112 + 20766785
ACUGGUUAUCGAUUGGCUACGGGCAGUAGCCAACACUGUCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCUGCGACGGUUGCAGUUUUCUUGAUACGCAGUUGAAAA
((((((.(((((((((((((.....)))))))).((((.((.(((((...((((....)))).....(((....))).))))).))))))....))))))).))))...... ( -37.30)
>DroPse_CAF1 3095 103 + 1
GUGUGCUAUCGAUUUCUUGCACUUGCUAUACAGCACUGC--------AAAUUCCAAUUGGAUUUUUUCAGUGU-CUUCGACUGGUGUAGUUUUUUUCGUGCGCAUUAGAAAA
((((((...(((....(((((((.........((((((.--------(((.(((....)))..))).))))))-........)))))))......))).))))))....... ( -26.83)
>DroEre_CAF1 3073 112 + 1
ACUGGUUAUCGAUUGGCUACUGGCAGUAGCCAACACUGCCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCUGCGACGGUUGCAGUUUUCUUGAUACGCAGUUGAGAA
((((((.(((((((((((((.....)))))))).(((((...(((((...((((....)))).....(((....))).)))))..)))))....))))))).))))...... ( -37.90)
>DroYak_CAF1 3076 112 + 1
ACUGGUUAUCGAUUGGCUACGGGCAGUAGCCAACACUGCCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCUGCGACGGUUGCAGUUUUCUUGAUACGCAGUUGAAAA
((((((.(((((((((((((.....)))))))).(((((...(((((...((((....)))).....(((....))).)))))..)))))....))))))).))))...... ( -38.40)
>DroAna_CAF1 3268 108 + 1
AA-AGUUAUCGAUUUAUGGAAUGCGCUUAUCAACACUGGUGCCAGUCAU--UCCAGUUGGAGUUUUUUAGUGUUCUUCGACGG-UGCAGUUUUCUUGGUGCGCAGCAGAAAA
..-.(((.........(((((((.((((((((....)))))..))))))--))))(((((((..(......)..))))))).(-((((.(......).))))))))...... ( -26.40)
>DroPer_CAF1 3099 103 + 1
GUGUGCUAUCGAUUUCUUGCAGUUGCUAGACAGCACUGC--------AAAUUCCAAUUGGAUUUUUUCAGUGU-CUUCGACUGGUGUAGUUUUUUUCGUGCGCAUUAGAAAA
((((((...(((....(((((((.(((....))))))))--------))((.(((((((((....))))))((-(...)))))).))........))).))))))....... ( -26.30)
>consensus
ACUGGUUAUCGAUUGGCUACAGGCACUAGCCAACACUGCCAUCCGUCAUUUUCCAGUUGGAGUUUUUCAGUGUUCUGCGACGGUUGCAGUUUUCUUGAUACGCAGUAGAAAA
........(((..........(((....)))(((((((.............(((....)))......)))))))...)))(((((((.((.........))))))))).... (-13.31 = -12.39 +  -0.91)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,056,246 – 11,056,358
Length 112
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 74.93
Mean single sequence MFE -29.53
Consensus MFE -7.61
Energy contribution -8.86
Covariance contribution 1.25
Combinations/Pair 1.12
Mean z-score -2.85
Structure conservation index 0.26
SVM decision value 0.92
SVM RNA-class probability 0.882946
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11056246 112 - 20766785
UUUUCAACUGCGUAUCAAGAAAACUGCAACCGUCGCAGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGACAGUGUUGGCUACUGCCCGUAGCCAAUCGAUAACCAGU
......((((..((((......((((((.(((((((((....)))......(((....)))...)))))).)).))))(((((((((.....))))))))).))))..)))) ( -37.30)
>DroPse_CAF1 3095 103 - 1
UUUUCUAAUGCGCACGAAAAAAACUACACCAGUCGAAG-ACACUGAAAAAAUCCAAUUGGAAUUU--------GCAGUGCUGUAUAGCAAGUGCAAGAAAUCGAUAGCACAC
.(((((..(((((.(((...............))).((-.(((((...((((((....)).))))--------.))))))).........))))))))))............ ( -19.76)
>DroEre_CAF1 3073 112 - 1
UUCUCAACUGCGUAUCAAGAAAACUGCAACCGUCGCAGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGGCAGUGUUGGCUACUGCCAGUAGCCAAUCGAUAACCAGU
......((((..((((......(((((..(((((((((....)))......(((....)))...))))))...)))))(((((((((.....))))))))).))))..)))) ( -39.20)
>DroYak_CAF1 3076 112 - 1
UUUUCAACUGCGUAUCAAGAAAACUGCAACCGUCGCAGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGGCAGUGUUGGCUACUGCCCGUAGCCAAUCGAUAACCAGU
......((((..((((......(((((..(((((((((....)))......(((....)))...))))))...)))))(((((((((.....))))))))).))))..)))) ( -38.90)
>DroAna_CAF1 3268 108 - 1
UUUUCUGCUGCGCACCAAGAAAACUGCA-CCGUCGAAGAACACUAAAAAACUCCAACUGGA--AUGACUGGCACCAGUGUUGAUAAGCGCAUUCCAUAAAUCGAUAACU-UU
(((((.((.(.(((..........))).-).)).)))))..................((((--(((((((....))))(((....))).))))))).............-.. ( -19.80)
>DroPer_CAF1 3099 103 - 1
UUUUCUAAUGCGCACGAAAAAAACUACACCAGUCGAAG-ACACUGAAAAAAUCCAAUUGGAAUUU--------GCAGUGCUGUCUAGCAACUGCAAGAAAUCGAUAGCACAC
........(((...(((............((((.....-..))))......(((....))).(((--------((((((((....))).))))))))...)))...)))... ( -22.20)
>consensus
UUUUCAACUGCGCACCAAGAAAACUGCAACCGUCGAAGAACACUGAAAAACUCCAACUGGAAAAUGACGGAUGGCAGUGUUGGCUACCGCCUGCAACAAAUCGAUAACCAGU
...............................((((...(((((((......(((....))).............)))))))(((....)))..........))))....... ( -7.61 =  -8.86 +   1.25)

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 10:50:47 2006