Locus 7513

Sequence ID 3R_DroMel_CAF1
Location 20,072,547 – 20,072,690
Length 143
Max. P 0.994833
window12133 window12134 window12135

overview

Window 3

Location 20,072,547 – 20,072,651
Length 104
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.08
Mean single sequence MFE -39.42
Consensus MFE -25.18
Energy contribution -27.38
Covariance contribution 2.20
Combinations/Pair 1.36
Mean z-score -1.31
Structure conservation index 0.64
SVM decision value 0.26
SVM RNA-class probability 0.658111
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20072547 104 + 27905053
---AUUUGGAGCGAUUGGUUCCAACCCAGCUAGCGGUAACAAUUCUGCGGCUGCCCAAGCCGCAGCUGCCGCCGCCGCCU-CGGCGAUGAUCGAUCGUCAGCAGCAGA
---..(((((((.....)))))))....(((.((((((......((((((((.....)))))))).)))))).((((...-))))(((((....))))))))...... ( -43.40)
>DroPse_CAF1 16664 89 + 1
CAAUUUCGGGGCCAUCGGCUCGAAU---GCUGGCGGAAGCAGU---------------GCAGCAGCAGCUGCGGCCGCUG-CAGCCAUGAUCGAUCGCCAGCAGCAGA
....((((((.(....).))))))(---((((((((..(((((---------------(((((....)))))....))))-)..))..((....)))))))))..... ( -38.00)
>DroSec_CAF1 14733 105 + 1
---AUUUGGAGGGAUUGGUUUCGACCCCCCUACGGGUAACAAUGCUGUUGAUCACAAAACUGAACUUGCCAACGCCGUCUGCGGCGAUGAUCGAUCGUCAGGAGCAGU
---(((((.((((...(((....))).)))).))))).....((((.(((((((......)))......((.(((((....))))).))........)))).)))).. ( -29.10)
>DroSim_CAF1 15964 104 + 1
---AUUUGGAGCGAUUGGUUCCAACCCAGCUAGCGGUAACAAUUCUGCGGCUGCCCAAGCCGCAGCUGCCGCCGCCGCCU-CGGCGAUGAUCGAUCGGCAGCAGCAGA
---..(((((((.....)))))))....(((..............(((((((.....)))))))((((((((((......-))))(((.....))))))))))))... ( -44.60)
>DroEre_CAF1 17356 104 + 1
---AUUUGGAGCGAUUGGUUCCAACCCAGUUAGCGGUAACAAUUCGGUGGCUGCCCAGGCCGCAGCUGCUGCCGCCGCCU-CGGCGAUGAUCGAUCGCCAGCAGCAGA
---..(((((((.....)))))))....(((.(((((.......(((..(((((.......)))))..)))..)))))..-.((((((.....)))))))))...... ( -39.50)
>DroYak_CAF1 15195 104 + 1
---AUUCGGAGCUAUUGGUUCCAACCCAGUAAGCGGCAACAAUUCGGUGGCUGCCCAGGCCGCAGCUGCUGCCGCCGCAU-CGGCGAUGAUCGAUCGCCAGCAGCAGA
---...((((((((((((.......))))).)))(....)..))))((((((.....)))))).((((((((....))..-.((((((.....))))))))))))... ( -41.90)
>consensus
___AUUUGGAGCGAUUGGUUCCAACCCAGCUAGCGGUAACAAUUCUGUGGCUGCCCAAGCCGCAGCUGCCGCCGCCGCCU_CGGCGAUGAUCGAUCGCCAGCAGCAGA
.....(((((((.....)))))))....(((.(((((.........((((((((.......))))))))...(((((....))))).......))))).)))...... (-25.18 = -27.38 +   2.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,072,584 – 20,072,690
Length 106
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 75.60
Mean single sequence MFE -40.62
Consensus MFE -22.59
Energy contribution -25.82
Covariance contribution 3.22
Combinations/Pair 1.13
Mean z-score -2.86
Structure conservation index 0.56
SVM decision value 2.52
SVM RNA-class probability 0.994833
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20072584 106 + 27905053
AAUUCUGCGGCUGCCCAAGCCGCAGCUGCCGC---CGCCGCCU-CGGCGAUGAUCGAUCGUCAGCAGCAGA-AUUUGCAGAAUCUGCAGACUUUGCAAAAUUUGCAAAGGA
..((((((((((.....)))))).(((((.((---((......-))))(((((....))))).))))))))-)(((((((...)))))))(((((((.....))))))).. ( -47.80)
>DroSec_CAF1 14770 108 + 1
AAUGCUGUUGAUCACAAAACUGAACUUGCCAA---CGCCGUCUGCGGCGAUGAUCGAUCGUCAGGAGCAGUUGUUUGCAGAAUAUGCAGACUUUGCAAAAUUUGCAAAGGA
..((((.(((((((......)))......((.---(((((....))))).))........)))).))))....((((((.....))))))(((((((.....))))))).. ( -33.00)
>DroSim_CAF1 16001 106 + 1
AAUUCUGCGGCUGCCCAAGCCGCAGCUGCCGC---CGCCGCCU-CGGCGAUGAUCGAUCGGCAGCAGCAGA-AUUUACAGAAUAUGCAGACUUUGCAAAAUUUGCAAAGGA
((((((((((((.....)))))).(((((.((---(((((...-))))(((.....)))))).))))))))-)))...............(((((((.....))))))).. ( -45.60)
>DroEre_CAF1 17393 106 + 1
AAUUCGGUGGCUGCCCAGGCCGCAGCUGCUGC---CGCCGCCU-CGGCGAUGAUCGAUCGCCAGCAGCAGA-AUUUGCAGAAUCUGCAGACUUUGCAAAAUUUGCAAAGGA
..(((....(((((..((((.((.((....))---.)).))))-.((((((.....)))))).))))).))-)(((((((...)))))))(((((((.....))))))).. ( -45.00)
>DroYak_CAF1 15232 106 + 1
AAUUCGGUGGCUGCCCAGGCCGCAGCUGCUGC---CGCCGCAU-CGGCGAUGAUCGAUCGCCAGCAGCAGA-AUUUGCAGAAUCUGCAGACAUUGCAAAACUUGCAACGGA
....(((..(((((.......)))))..)))(---((..(((.-.((((((.....))))))....((((.-.(((((((...)))))))..))))......)))..))). ( -42.20)
>DroMoj_CAF1 18837 96 + 1
----CGGUGCCCGCCUUAGCAGCAGCGGCUGCAAUAGCCAAUG-CAGCAAUAAUUGAUCGGCAGGUUCAGG-ACAUGCAGCGUCUGCAGCGU-------CUUUAUGAC--A
----..(.(((.(((...((....)).((((((........))-))))...........))).))).)(((-((.(((((...)))))..))-------)))......--. ( -30.10)
>consensus
AAUUCGGUGGCUGCCCAAGCCGCAGCUGCCGC___CGCCGCCU_CGGCGAUGAUCGAUCGCCAGCAGCAGA_AUUUGCAGAAUCUGCAGACUUUGCAAAAUUUGCAAAGGA
......((((((.....)))))).(((((.......((((....))))(((.....)))....))))).....((((((.....))))))(((((((.....))))))).. (-22.59 = -25.82 +   3.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,072,584 – 20,072,690
Length 106
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 75.60
Mean single sequence MFE -41.67
Consensus MFE -22.69
Energy contribution -24.70
Covariance contribution 2.01
Combinations/Pair 1.27
Mean z-score -2.85
Structure conservation index 0.54
SVM decision value 2.50
SVM RNA-class probability 0.994657
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20072584 106 - 27905053
UCCUUUGCAAAUUUUGCAAAGUCUGCAGAUUCUGCAAAU-UCUGCUGCUGACGAUCGAUCAUCGCCG-AGGCGGCG---GCGGCAGCUGCGGCUUGGGCAGCCGCAGAAUU
..(((((((.....)))))))..(((((...)))))(((-(((((.(((((.((....)).))(((.-((((.(((---((....))))).)))).)))))).)))))))) ( -49.40)
>DroSec_CAF1 14770 108 - 1
UCCUUUGCAAAUUUUGCAAAGUCUGCAUAUUCUGCAAACAACUGCUCCUGACGAUCGAUCAUCGCCGCAGACGGCG---UUGGCAAGUUCAGUUUUGUGAUCAACAGCAUU
..(((((((.....)))))))..((((.....))))...........(((..((((...((.(((((....)))))---.))(((((......)))))))))..))).... ( -29.00)
>DroSim_CAF1 16001 106 - 1
UCCUUUGCAAAUUUUGCAAAGUCUGCAUAUUCUGUAAAU-UCUGCUGCUGCCGAUCGAUCAUCGCCG-AGGCGGCG---GCGGCAGCUGCGGCUUGGGCAGCCGCAGAAUU
..(((((((.....)))))))..((((.....))))...-.((((((((((((.(((........))-)..)))))---)))))))((((((((.....)))))))).... ( -49.50)
>DroEre_CAF1 17393 106 - 1
UCCUUUGCAAAUUUUGCAAAGUCUGCAGAUUCUGCAAAU-UCUGCUGCUGGCGAUCGAUCAUCGCCG-AGGCGGCG---GCAGCAGCUGCGGCCUGGGCAGCCACCGAAUU
..(((((((.....)))))))..(((((...)))))(((-((.((((((((((((.....)))))).-((((.(((---((....))))).)))).))))))....))))) ( -48.20)
>DroYak_CAF1 15232 106 - 1
UCCGUUGCAAGUUUUGCAAUGUCUGCAGAUUCUGCAAAU-UCUGCUGCUGGCGAUCGAUCAUCGCCG-AUGCGGCG---GCAGCAGCUGCGGCCUGGGCAGCCACCGAAUU
..(((((((.....)))))))..(((((...)))))(((-((((((((((.((((((........))-)).)).))---))))))(((((.......)))))....))))) ( -42.90)
>DroMoj_CAF1 18837 96 - 1
U--GUCAUAAAG-------ACGCUGCAGACGCUGCAUGU-CCUGAACCUGCCGAUCAAUUAUUGCUG-CAUUGGCUAUUGCAGCCGCUGCUGCUAAGGCGGGCACCG----
.--........(-------(((.(((((...))))))))-).....((((((...........((((-((........)))))).((....))...)))))).....---- ( -31.00)
>consensus
UCCUUUGCAAAUUUUGCAAAGUCUGCAGAUUCUGCAAAU_UCUGCUGCUGACGAUCGAUCAUCGCCG_AGGCGGCG___GCAGCAGCUGCGGCUUGGGCAGCCACAGAAUU
..(((((((.....))))))).((((.....(((((.....(((((((....(((.....)))((((....))))....))))))).))))).....)))).......... (-22.69 = -24.70 +   2.01)

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 12:47:47 2006