Locus 1386

Sequence ID 3R_DroMel_CAF1
Location 4,049,119 – 4,049,227
Length 108
Max. P 0.681721
window2284 window2285

overview

Window 4

Location 4,049,119 – 4,049,227
Length 108
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.28
Mean single sequence MFE -32.87
Consensus MFE -21.68
Energy contribution -22.35
Covariance contribution 0.67
Combinations/Pair 1.25
Mean z-score -1.39
Structure conservation index 0.66
SVM decision value -0.03
SVM RNA-class probability 0.518878
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4049119 108 + 27905053
AAAUCGCUUGGCAAUUAAAUAACUUCACACCGCGCGCUAAGUGGGCGUGGC--AGCAAACGCCCACACACGCCCAAAAAUUUCGCAUUUG-AAAUGUAAAGCGCACGCGGC
.............................(((((.((...((((((((...--.....))))))))....((......((((((....))-)))).....)))).))))). ( -33.70)
>DroPse_CAF1 33978 109 + 1
AAAACGCUUGGCAAUUAAAUAACUUCACACCGCGCGCUGAAUGGGCGUGUCGCUGUGGACGCCCACCCCCGCCCCAGGAU-UCGCAUUUG-AAAUGUGAAGCGCACGCGGC
....(((...((...........((((((.((((((((.....)))))).)).)))))).((......((......)).(-((((((...-..)))))))))))..))).. ( -32.90)
>DroEre_CAF1 38977 108 + 1
AAAUCGCUUGGCAAUUAAAUAACUUCACACCGCGCGCUAAGUGGGCGUGGC--CGCCGACGCCCACACACGCCCAGAAAUUUCGCAUUUG-AAAUGUAAAGUGCACGCGGC
.............................(((((((....((((((((.(.--...).))))))))...)))...........((((((.-.......))))))..)))). ( -32.80)
>DroWil_CAF1 63278 97 + 1
UAAACGCUUAGCAAUUAAAUAACUUCACACUGUGCUCGAAAUGGGCGUGAA----------CCCGC-CACGCCCCUUCA---UGCAUUUGCGAAUGUGAAGCGCACGCGGC
....(((((.(((..........(((.((..((((..(((..(((((((..----------.....-))))))).))).---.)))).)).)))))).)))))........ ( -28.40)
>DroAna_CAF1 39584 108 + 1
AAAACGCUUGGCAAUUAAAUAAAUUCACACCGCAAGCUGUGUGGGCGUGGC--CAGUUCCGCCCACCACCGCCCAAAAAUUUCGCAUUUG-AAAUGUAAAGCGCACGCGGC
....((((((((..............(((.(....).)))(((((((..(.--...)..)))))))....))).....((((((....))-))))...)))))........ ( -29.90)
>DroPer_CAF1 34414 109 + 1
AAAACGCUUGGCAAUUAAAUAACUUCACACCGCGCGCUGAAUGGGCGUGUCGGUGUGGACGCCCACCCCCGCCCCAGGAU-UCGCAUUUG-AAAUGUGAAGCGCACGCGGC
....(((...((...........(((((((((((((((.....)))))).))))))))).((......((......)).(-((((((...-..)))))))))))..))).. ( -39.50)
>consensus
AAAACGCUUGGCAAUUAAAUAACUUCACACCGCGCGCUAAAUGGGCGUGGC__CGCGGACGCCCACCCACGCCCAAAAAU_UCGCAUUUG_AAAUGUAAAGCGCACGCGGC
.............................(((((.((....(((((((.(......).)))))))..................(((((....))))).....)).))))). (-21.68 = -22.35 +   0.67)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 4,049,119 – 4,049,227
Length 108
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 81.28
Mean single sequence MFE -39.40
Consensus MFE -26.29
Energy contribution -26.48
Covariance contribution 0.20
Combinations/Pair 1.15
Mean z-score -1.70
Structure conservation index 0.67
SVM decision value 0.31
SVM RNA-class probability 0.681721
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4049119 108 - 27905053
GCCGCGUGCGCUUUACAUUU-CAAAUGCGAAAUUUUUGGGCGUGUGUGGGCGUUUGCU--GCCACGCCCACUUAGCGCGCGGUGUGAAGUUAUUUAAUUGCCAAGCGAUUU
(((((((((((((...((((-(......)))))....))))....((((((((.....--...))))))))...)))))))))............((((((...)))))). ( -41.60)
>DroPse_CAF1 33978 109 - 1
GCCGCGUGCGCUUCACAUUU-CAAAUGCGA-AUCCUGGGGCGGGGGUGGGCGUCCACAGCGACACGCCCAUUCAGCGCGCGGUGUGAAGUUAUUUAAUUGCCAAGCGUUUU
(((((((((((((((...((-(......))-)...))))))..((((((((((..........)))))))))).)))))))))............................ ( -42.50)
>DroEre_CAF1 38977 108 - 1
GCCGCGUGCACUUUACAUUU-CAAAUGCGAAAUUUCUGGGCGUGUGUGGGCGUCGGCG--GCCACGCCCACUUAGCGCGCGGUGUGAAGUUAUUUAAUUGCCAAGCGAUUU
(((((((((.......((((-(......)))))...((((((((.((.(.(...).).--))))))))))....)))))))))............((((((...)))))). ( -40.60)
>DroWil_CAF1 63278 97 - 1
GCCGCGUGCGCUUCACAUUCGCAAAUGCA---UGAAGGGGCGUG-GCGGG----------UUCACGCCCAUUUCGAGCACAGUGUGAAGUUAUUUAAUUGCUAAGCGUUUA
..(((..((((((((((((.(....(((.---((((((((((((-(....----------.)))))))).))))).)))))))))))))).........))...))).... ( -35.60)
>DroAna_CAF1 39584 108 - 1
GCCGCGUGCGCUUUACAUUU-CAAAUGCGAAAUUUUUGGGCGGUGGUGGGCGGAACUG--GCCACGCCCACACAGCUUGCGGUGUGAAUUUAUUUAAUUGCCAAGCGUUUU
((((((.((((((...((((-(......)))))....)))).(((.((((((......--....))))))))).)).))))))............................ ( -33.60)
>DroPer_CAF1 34414 109 - 1
GCCGCGUGCGCUUCACAUUU-CAAAUGCGA-AUCCUGGGGCGGGGGUGGGCGUCCACACCGACACGCCCAUUCAGCGCGCGGUGUGAAGUUAUUUAAUUGCCAAGCGUUUU
(((((((((((((((...((-(......))-)...))))))..((((((((((..........)))))))))).)))))))))............................ ( -42.50)
>consensus
GCCGCGUGCGCUUCACAUUU_CAAAUGCGA_AUUUUGGGGCGGGGGUGGGCGUCCACA__GCCACGCCCACUCAGCGCGCGGUGUGAAGUUAUUUAAUUGCCAAGCGUUUU
..(((((((((..............(((...........)))...(((((((............)))))))...))))))(((.((((....))))...)))..))).... (-26.29 = -26.48 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:46 2006