Locus 6142

Sequence ID 2R_DroMel_CAF1
Location 19,333,849 – 19,334,085
Length 236
Max. P 0.967275
window9836 window9837 window9838

overview

Window 6

Location 19,333,849 – 19,333,957
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -39.75
Consensus MFE -27.19
Energy contribution -26.75
Covariance contribution -0.44
Combinations/Pair 1.25
Mean z-score -2.75
Structure conservation index 0.68
SVM decision value 1.61
SVM RNA-class probability 0.967275
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19333849 108 + 20766785
--GGCAGCGGGCGGUGCAAUAGAACGUGAAAAUCUGUUUUCCUAUAGCAUUUUCCGGGUGCG----------GGAAAAGCUUGGGAAAGCAGGGGCAACUUCGUUGCAUCGGUACAAAUU
--.......(.(((((((((.(((.((.....((((((((((((.(((.(((((((....))----------))))).)))))))))))))))....)))))))))))))).)....... ( -43.10)
>DroSec_CAF1 11809 108 + 1
--GGCAGCGGGCGGUGCAAUAGAACGUGAAAAUCUGUUUUCCUCCAGCAUUUUCCGGGUGCG----------GGGAAAGCUUGGGAAAGCAGGGGCAACUUCGUUGCAUCGGUACAAAUU
--.......(.(((((((((.(((.((.....(((((((((((..(((.((..(((....))----------)..)).))).)))))))))))....)))))))))))))).)....... ( -41.10)
>DroSim_CAF1 11895 108 + 1
--GGCAGCGGGCGGUGCAAUAGAACGUGAAAAUCUGUUUUCCUCUAGCAUUUUCCGGGUGCG----------GGGAAAGCUUGGGAAAGCAGGGGCAACUUCGUUGCAUCGCUACAAAUU
--.......(((((((((((.(((.((.....(((((((((((..(((.((..(((....))----------)..)).))).)))))))))))....))))))))))))))))....... ( -46.50)
>DroEre_CAF1 11939 117 + 1
GGUGGAGCAGACGAUGCAAUAGAACGUGAAAAUCUGUUUUCCUCCAGCAUUUUCCGGGGGCAGGGGCAG-CUGGAAAAGCUUGGGAA--CAGGGGCAACUUCGUUGCAUCGCCACAAACU
.((((......(((((((((.(((.((.....(((((((.((...(((.((((((((..((....))..-))))))))))).)))))--))))....))))))))))))))))))..... ( -43.30)
>DroYak_CAF1 12174 116 + 1
--GGCAGCAGGCGAUGCAAUAGAACGUGAAAAUCUGUUUUCCUCUAGCAUUUUCCGGGGGGAGGAGAGGACAGGAGAAGCUGGGGAA--CAGAGGUAACUUCGUUGCAUCAAGACAAAUU
--.((.....))((((((((.(((.((.....(((((..(((.(((((.((((((..(............).)))))))))))))))--))))....))))))))))))).......... ( -36.50)
>DroAna_CAF1 13069 108 + 1
--GGCUAGGAGCGAUGCAAUAGAACGUGAAAAUCUGUUUUCCGCAGGCGUUUCUAUGGCUUA------AA--CAGAAAAGUAGGGAA--CGGUGACAACUUCGUUGCAUCGAAACAAAUU
--.....(...(((((((((.(((..((....(((((.....)))))(((((((...((((.------..--.....)))).)))))--))....))..))))))))))))...)..... ( -28.00)
>consensus
__GGCAGCGGGCGAUGCAAUAGAACGUGAAAAUCUGUUUUCCUCUAGCAUUUUCCGGGUGCA__________GGAAAAGCUUGGGAA__CAGGGGCAACUUCGUUGCAUCGAUACAAAUU
...........(((((((((.(((.((.....((((..((((.(.(((.((((((.................))))))))).)))))..))))....))))))))))))))......... (-27.19 = -26.75 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,333,957 – 19,334,062
Length 105
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 78.85
Mean single sequence MFE -25.72
Consensus MFE -11.04
Energy contribution -12.84
Covariance contribution 1.80
Combinations/Pair 1.19
Mean z-score -2.42
Structure conservation index 0.43
SVM decision value 1.22
SVM RNA-class probability 0.932889
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19333957 105 + 20766785
UGUGUGCGUGCGCUUGGCCUC-----------AUGCAGCUAUACGAGUAUAGCAUGUAUCCACACUA--UAUAGCUAUAUCUAUAUCUAUAGCUUUAGCUCCUGCAAAACUGAAUAAU
.(((((.((((((.((....)-----------).)).((((((....))))))..)))).)))))..--((.(((((((........))))))).))((....))............. ( -27.80)
>DroSec_CAF1 11917 96 + 1
UGUGUGCGUGCGCUUGGCCUC-----------AUGCAGCUA--------UAGUAUGUAUCCACA-UA--UAUAGCUAUAUCUAUAUCUAUAGCUAUAGCUCCUGCAAAACUGAAUAAU
(((((((((((...((((...-----------.....))))--------..)))))))..))))-..--((((((((((........))))))))))((....))............. ( -25.70)
>DroSim_CAF1 12003 96 + 1
UGUGUGCGUGCGCUUGGCCUC-----------AUGCAACUA--------UAGUAUGUAUCCACA-UG--UAUAGCUAUAUCUAUAUCUAUAGCUAUAGCUCCUGCAAAACUGAAUAAU
....((((((((..(((...(-----------((((.....--------..)))))...)))..-))--)))(((((((.((((....)))).)))))))...)))............ ( -23.50)
>DroEre_CAF1 12056 100 + 1
UGUGUGCGUGCGCUUGGCCUCUGUCGAUGGUCACGCAGCUA--------U---AUGUAUCCACA-------CAGAUAUAUCUAUAUCUAUAUCUAUAGCUCACGCAAAACUGAAUAAU
....((((((.((.(((((((....)).))))).))(((((--------(---(.((((.....-------.((((((....)))))))))).)))))))))))))............ ( -29.60)
>DroYak_CAF1 12290 106 + 1
UGUGUGCGUGCGCUUGGCCUCCGUCGAUGGUCAUCCACACA--------U---AUACAUACAUA-UAUCUACGAGUAUAUCUAUAUCUAUAGCUAUAGCUCCCGCAAAACUGAAUAAU
((((((.(((.(..(((((((....)).)))))..).))).--------)---)))))......-.......(((((((.((((....)))).))).))))................. ( -22.00)
>consensus
UGUGUGCGUGCGCUUGGCCUC___________AUGCAGCUA________UAG_AUGUAUCCACA_UA__UAUAGCUAUAUCUAUAUCUAUAGCUAUAGCUCCUGCAAAACUGAAUAAU
...((...((((...(((..............(((((((((((....)))))).))))).............(((((((........)))))))...)))..))))..))........ (-11.04 = -12.84 +   1.80)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,333,985 – 19,334,085
Length 100
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 85.66
Mean single sequence MFE -23.73
Consensus MFE -18.88
Energy contribution -19.38
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.80
SVM decision value 0.48
SVM RNA-class probability 0.753873
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19333985 100 - 20766785
CAAGUGCUCGACGGGCGCUAUCGAUUAUUCAGUUUUGCAGGAGCUAAAGCUAUAGAUAUAGAUAUAGCUAUA--UAGUGUGGAUACAUGCUAUACUCGUAUA
..((((((.....))))))..(((......(((((.....)))))..(((((((........))))))).((--(((((((....))))))))).))).... ( -26.70)
>DroSec_CAF1 11945 91 - 1
CAAGUGCUCGACGGGCGCUAUUGAUUAUUCAGUUUUGCAGGAGCUAUAGCUAUAGAUAUAGAUAUAGCUAUA--UA-UGUGGAUACAUACUA--------UA
..((((((.....))))))(((((....)))))((..((..(((((((.((((....)))).)))))))...--..-))..)).........--------.. ( -24.20)
>DroSim_CAF1 12031 91 - 1
CAAGUGCUCGACGGGCGCUAUCGAUUAUUCAGUUUUGCAGGAGCUAUAGCUAUAGAUAUAGAUAUAGCUAUA--CA-UGUGGAUACAUACUA--------UA
..((((((.....))))))............((((..(((.(((((((.((((....)))).)))))))...--).-))..)).))......--------.. ( -23.30)
>DroYak_CAF1 12329 90 - 1
CAAGUGCUCGACGGGCGCUAUCGAUUAUUCAGUUUUGCGGGAGCUAUAGCUAUAGAUAUAGAUAUACUCGUAGAUA-UAUGUAUGUAU---A--------UG
..((((((.....))))))(((((....))((((..((....))...))))...)))....((((((.((((....-))))...))))---)--------). ( -20.70)
>consensus
CAAGUGCUCGACGGGCGCUAUCGAUUAUUCAGUUUUGCAGGAGCUAUAGCUAUAGAUAUAGAUAUAGCUAUA__UA_UGUGGAUACAUACUA________UA
..((((((.....))))))......((((((.....((....))((((((((((........)))))))))).......))))))................. (-18.88 = -19.38 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:50 2006