Locus 3645

Sequence ID 3R_DroMel_CAF1
Location 9,842,824 – 9,842,949
Length 125
Max. P 0.989900
window5858 window5859 window5860

overview

Window 8

Location 9,842,824 – 9,842,922
Length 98
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 86.45
Mean single sequence MFE -22.68
Consensus MFE -19.12
Energy contribution -19.62
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -2.74
Structure conservation index 0.84
SVM decision value 2.19
SVM RNA-class probability 0.989900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9842824 98 - 27905053
CAUCCGUGCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCUCUCUAUUUCCCCAUUCUAUUUGCCCAUUUCGAAGCUAC----AUA
..((((.......)))).(((((((.(((....))))))))))...((((((((................................)))))))).----... ( -23.45)
>DroSec_CAF1 48869 102 - 1
GACCCGUGCACAUUGGAAGGGCAUUUUGCUACUGCAAAUGCCCCAUUAGCUUUGUCUCUCUAUUUCCCCAUUCUAUUUGCCCAUUUCGAAGCUACAUACAUA
...(((.......)))..((((((((.((....))))))))))...((((((((................................))))))))........ ( -21.85)
>DroEre_CAF1 49880 96 - 1
CAUCCAUGCUCUUUGGAAGGGCAUUGAGCUACUGCACAGACCCCAUUAGCUUUGUGU--GUACUUCCCCAUUCUAUUUGCCCAUUUCAAAGCUAC----AAA
..........(((((((((((((..(((.(((.(((((((.(......).)))))))--))).)))...........))))).))))))))....----... ( -22.52)
>DroYak_CAF1 50393 96 - 1
AACCCAUUCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCU--CCACUUCCCCAAUCUAUUUGCCCAUUUCAAAGCUAC----AAA
...(((.......)))..(((((((.(((....))))))))))...((((((((...--...........................)))))))).----... ( -22.91)
>consensus
CACCCAUGCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCU__CUACUUCCCCAUUCUAUUUGCCCAUUUCAAAGCUAC____AAA
...(((.......)))..(((((((.(((....))))))))))...((((((((................................))))))))........ (-19.12 = -19.62 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,842,852 – 9,842,949
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 83.10
Mean single sequence MFE -26.77
Consensus MFE -19.65
Energy contribution -19.84
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.73
SVM decision value -0.01
SVM RNA-class probability 0.529603
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9842852 97 + 27905053
UGGGGAAAUAGAGAGACAAAGCUAAUGGGGCAUUUGCAGUAGCACAAUGCCCUUCCAAUGUGCACGGAUGUAUAUUUUCUGAGAUGCCCUUCAAAAU
.((((...(((((((...........(((((((((((....))).)))))))).....((((((....))))))))))))).....))))....... ( -27.00)
>DroSec_CAF1 48901 97 + 1
UGGGGAAAUAGAGAGACAAAGCUAAUGGGGCAUUUGCAGUAGCAAAAUGCCCUUCCAAUGUGCACGGGUCUAUCUUUUCUGAGAUGCCCUCUAAAUU
...(((((.(((.((((...((....(((((((((((....)).)))))))))........))....)))).))))))))(((.....)))...... ( -27.60)
>DroEre_CAF1 49908 95 + 1
UGGGGAAGUAC--ACACAAAGCUAAUGGGGUCUGUGCAGUAGCUCAAUGCCCUUCCAAAGAGCAUGGAUGUAUCUUUUGUUAGAUGCCCUAGAAAAU
(((((...(((--(..((..(((...(((((.((.((....)).))..))))).......))).))..))))(((......)))..)))))...... ( -22.50)
>DroYak_CAF1 50421 89 + 1
UGGGGAAGUGG--AGACAAAGCUAAUGGGGCAUUUGCAGUAGCACAAUGCCCUUCCAAUGUGAAUGGGUUUAUCUUUUCUGAGCUGCCCUA------
(((((.(((..--(((.((((.(((.(((((((((((....))).))))))))((((.......)))).))).)))))))..))).)))))------ ( -30.00)
>consensus
UGGGGAAAUAG__AGACAAAGCUAAUGGGGCAUUUGCAGUAGCACAAUGCCCUUCCAAUGUGCACGGAUGUAUCUUUUCUGAGAUGCCCUA_AAAAU
.((((........(((.((((.((..(((((((((((....))).))))))))(((.........)))..)).)))))))......))))....... (-19.65 = -19.84 +   0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,842,852 – 9,842,949
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 83.10
Mean single sequence MFE -24.07
Consensus MFE -17.28
Energy contribution -17.91
Covariance contribution 0.63
Combinations/Pair 1.09
Mean z-score -1.91
Structure conservation index 0.72
SVM decision value 0.69
SVM RNA-class probability 0.823090
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9842852 97 - 27905053
AUUUUGAAGGGCAUCUCAGAAAAUAUACAUCCGUGCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCUCUCUAUUUCCCCA
.....((..((((................((((.......)))).(((((((.(((....)))))))))).........))))..)).......... ( -23.20)
>DroSec_CAF1 48901 97 - 1
AAUUUAGAGGGCAUCUCAGAAAAGAUAGACCCGUGCACAUUGGAAGGGCAUUUUGCUACUGCAAAUGCCCCAUUAGCUUUGUCUCUCUAUUUCCCCA
........(((.......(((((((.(((((((.......)))..((((((((.((....))))))))))..........)))).))).))))))). ( -26.31)
>DroEre_CAF1 49908 95 - 1
AUUUUCUAGGGCAUCUAACAAAAGAUACAUCCAUGCUCUUUGGAAGGGCAUUGAGCUACUGCACAGACCCCAUUAGCUUUGUGU--GUACUUCCCCA
.......(((((((..................)))))))..(((((..(((.((((((.((.........)).))))))...))--)..)))))... ( -22.17)
>DroYak_CAF1 50421 89 - 1
------UAGGGCAGCUCAGAAAAGAUAAACCCAUUCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCU--CCACUUCCCCA
------..(((.((...(((((((.(((..(((.......)))..(((((((.(((....))))))))))..))).)))).)))--...)).))).. ( -24.60)
>consensus
AUUUU_UAGGGCAUCUCAGAAAAGAUACACCCAUGCACAUUGGAAGGGCAUUGUGCUACUGCAAAUGCCCCAUUAGCUUUGUCU__CUACUUCCCCA
........(((......(((((((......(((.......)))..(((((((.(((....))))))))))......)))).))).........))). (-17.28 = -17.91 +   0.63)

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 11:06:27 2006