Locus 2560

Sequence ID 2R_DroMel_CAF1
Location 9,077,079 – 9,077,190
Length 111
Max. P 0.718196
window4215 window4216

overview

Window 5

Location 9,077,079 – 9,077,190
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.47
Mean single sequence MFE -40.40
Consensus MFE -29.10
Energy contribution -30.44
Covariance contribution 1.34
Combinations/Pair 1.09
Mean z-score -1.98
Structure conservation index 0.72
SVM decision value 0.39
SVM RNA-class probability 0.718196
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077079 111 + 20766785
UGACAUACUGACCGCAGAGAGUGUACUUGAGCAAG-GGACUUCCCCGUGAAUCUGCCCGCCUGCUCAAGUGCUACGUAAUUUGCAUGGUCUGGAUUUUUUCAAAUUACAUGA--------
...(((...(((((((((..(((((((((((((.(-((.....)))(((........))).))))))))))).))....)))))..))))((((....))))......))).-------- ( -36.10)
>DroEre_CAF1 49346 116 + 1
UGGCAUACUGACCGCAGGGAGUGUACUUGAGCAGGG--GCUUCCCCGUGAAUCUGUCCGCCUGCUCAAGUGCUACACA-U-GGCAUGGUCUGGAUUUUGUCAAAUUACGCGAUGCUAUGA
.......(((....)))...((((((((((((((((--(....)))(((........))))))))))))))).)).((-(-(((((.((...(((((....)))))..)).)))))))). ( -42.40)
>DroYak_CAF1 45133 117 + 1
UGGCAUACUGACCGCAGGCAGUGUACUUGAGCUGGG--GCUUCCCCGUGAAGCUGUUCGCCUGCUCAAGUGCUACACA-UUUGCAUGGUCUGGAUUUUGUCGAAUUACGCGAUGCCAUGA
((((...(.(((((((((..((((((((((((.(((--(...))))(((((....)))))..)))))))))).))...-)))))..)))).)......((((.......))))))))... ( -42.70)
>consensus
UGGCAUACUGACCGCAGGGAGUGUACUUGAGCAGGG__GCUUCCCCGUGAAUCUGUCCGCCUGCUCAAGUGCUACACA_UUUGCAUGGUCUGGAUUUUGUCAAAUUACGCGAUGC_AUGA
(((((..(.(((((((((..(((((((((((((((...((..............))...))))))))))))).))....)))))..)))).).....))))).................. (-29.10 = -30.44 +   1.34)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 6

Location 9,077,079 – 9,077,190
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.47
Mean single sequence MFE -36.37
Consensus MFE -25.67
Energy contribution -26.45
Covariance contribution 0.78
Combinations/Pair 1.09
Mean z-score -1.80
Structure conservation index 0.71
SVM decision value 0.10
SVM RNA-class probability 0.585462
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9077079 111 - 20766785
--------UCAUGUAAUUUGAAAAAAUCCAGACCAUGCAAAUUACGUAGCACUUGAGCAGGCGGGCAGAUUCACGGGGAAGUCC-CUUGCUCAAGUACACUCUCUGCGGUCAGUAUGUCA
--------.......((((....))))...(((.((((......(((((.(((((((((((.((((...(((.....)))))))-))))))))))).......)))))....))))))). ( -31.30)
>DroEre_CAF1 49346 116 - 1
UCAUAGCAUCGCGUAAUUUGACAAAAUCCAGACCAUGCC-A-UGUGUAGCACUUGAGCAGGCGGACAGAUUCACGGGGAAGC--CCCUGCUCAAGUACACUCCCUGCGGUCAGUAUGCCA
.....((((.((((......))........((((..((.-.-.((((...(((((((((((.((.....(((.....))).)--)))))))))))))))).....)))))).)))))).. ( -36.20)
>DroYak_CAF1 45133 117 - 1
UCAUGGCAUCGCGUAAUUCGACAAAAUCCAGACCAUGCAAA-UGUGUAGCACUUGAGCAGGCGAACAGCUUCACGGGGAAGC--CCCAGCUCAAGUACACUGCCUGCGGUCAGUAUGCCA
...((((((.((((......))........((((..(((..-.((((...((((((((((((.....))))...((((...)--))).))))))))))))....))))))).)))))))) ( -41.60)
>consensus
UCAU_GCAUCGCGUAAUUUGACAAAAUCCAGACCAUGCAAA_UGUGUAGCACUUGAGCAGGCGGACAGAUUCACGGGGAAGC__CCCUGCUCAAGUACACUCCCUGCGGUCAGUAUGCCA
..........(((((((((....))))...((((..(((....((((...(((((((((((........(((.....))).....)))))))))))))))....)))))))..))))).. (-25.67 = -26.45 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:05 2006