Locus 5030

Sequence ID 3L_DroMel_CAF1
Location 13,791,488 – 13,791,621
Length 133
Max. P 0.925654
window7962 window7963 window7964

overview

Window 2

Location 13,791,488 – 13,791,586
Length 98
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -19.68
Consensus MFE -18.62
Energy contribution -18.62
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.95
SVM decision value 0.76
SVM RNA-class probability 0.842411
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13791488 98 + 23771897
AAGAAUUAGUAUUCAUGCCCCACAGUGUCAUUUCCGCGAAUGCGUGCGGGCGCAGAAAACUGGCAAAAAA--AA----------GAACAGAAAUGGAAAAAAGAAAAACU
.....(((((.(((.((((((.((.((.(((((....))))))))).))).)))))).))))).......--..----------...((....))............... ( -20.00)
>DroSec_CAF1 28532 100 + 1
AAGAAUUAGUAUUCAUGCCCCACAGUGUCAUUUCCGAGAAUGCGUGCGGGCGCAGAAGACUGGCAAAAAAAAAA----------AAACACAAAUCGAAAAAAGAAAAACU
.....(((((.(((.((((((.((.((.(((((....))))))))).))).)))))).)))))...........----------.......................... ( -18.70)
>DroSim_CAF1 24696 98 + 1
AAGAAUUAGUAUUCAUGCCCCACAGUGUCAUUUCCGCGAAUGCGUGCGGGCGCAGAAGACUGGCAAAAAA--AA----------GAACAGAAAUGGAAAAAAGAAAAACU
.....(((((.(((.((((((.((.((.(((((....))))))))).))).)))))).))))).......--..----------...((....))............... ( -20.00)
>DroEre_CAF1 27976 110 + 1
AAGAAUUAGUAUUCAUGCCCCACAGUGUCAUUUCCGCGAAUGCGUGCGGGCGCAGAAGACUGGCAAAAAAGAAAAAAAAGUAAAGCACAGAAAUGGAAAAAAGAAAAACU
.....(((((.(((.((((((.((.((.(((((....))))))))).))).)))))).)))))........................((....))............... ( -20.00)
>consensus
AAGAAUUAGUAUUCAUGCCCCACAGUGUCAUUUCCGCGAAUGCGUGCGGGCGCAGAAGACUGGCAAAAAA__AA__________GAACAGAAAUGGAAAAAAGAAAAACU
.....(((((.(((.((((((.((.((.(((((....))))))))).))).)))))).)))))............................................... (-18.62 = -18.62 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,791,528 – 13,791,621
Length 93
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 90.47
Mean single sequence MFE -20.07
Consensus MFE -17.48
Energy contribution -17.48
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.87
SVM decision value 1.17
SVM RNA-class probability 0.925654
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13791528 93 + 23771897
UGCGUGCGGGCGCAGAAAACUGGCAAAAAA--AA----------GAACAGAAAUGGAAAAAAGAAAAACUUUUUGCAAGCAUUUCUUGAUGGGAAUGGCGUGAGA
.((((((..((.(((....)))))......--..----------...((....))..((((((.....))))))))...(((((((....))))))))))).... ( -18.70)
>DroSec_CAF1 28572 95 + 1
UGCGUGCGGGCGCAGAAGACUGGCAAAAAAAAAA----------AAACACAAAUCGAAAAAAGAAAAACUUUUUGCAAGCAUUUCUUGAUGGGAAUGGCGUGAGA
.((((((..((.(((....)))))..........----------.............((((((.....))))))))...(((((((....))))))))))).... ( -17.70)
>DroSim_CAF1 24736 93 + 1
UGCGUGCGGGCGCAGAAGACUGGCAAAAAA--AA----------GAACAGAAAUGGAAAAAAGAAAAACUUUUUGCAAGCAUUUCUUGAUGGGAAUGGCGUGAGA
.((((((..((.(((....)))))......--..----------...((....))..((((((.....))))))))...(((((((....))))))))))).... ( -18.70)
>DroEre_CAF1 28016 105 + 1
UGCGUGCGGGCGCAGAAGACUGGCAAAAAAGAAAAAAAAGUAAAGCACAGAAAUGGAAAAAAGAAAAACUUUUUGCCAGCAUUUCUUGAUGGGAAUGGCGUGAGA
(((((....))))).....((((((((((..........(.....).((....))..............))))))))))(((((((....))))))).(....). ( -25.20)
>consensus
UGCGUGCGGGCGCAGAAGACUGGCAAAAAA__AA__________GAACAGAAAUGGAAAAAAGAAAAACUUUUUGCAAGCAUUUCUUGAUGGGAAUGGCGUGAGA
.((((((..((.(((....))))).................................((((((.....))))))))...(((((((....))))))))))).... (-17.48 = -17.48 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,791,528 – 13,791,621
Length 93
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 90.47
Mean single sequence MFE -14.82
Consensus MFE -11.62
Energy contribution -11.88
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.78
SVM decision value 0.16
SVM RNA-class probability 0.610439
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13791528 93 - 23771897
UCUCACGCCAUUCCCAUCAAGAAAUGCUUGCAAAAAGUUUUUCUUUUUUCCAUUUCUGUUC----------UU--UUUUUUGCCAGUUUUCUGCGCCCGCACGCA
......((...........(((((.(((.((((((((........................----------..--)))))))).))))))))((....))..)). ( -13.77)
>DroSec_CAF1 28572 95 - 1
UCUCACGCCAUUCCCAUCAAGAAAUGCUUGCAAAAAGUUUUUCUUUUUUCGAUUUGUGUUU----------UUUUUUUUUUGCCAGUCUUCUGCGCCCGCACGCA
....((((...((.....((((((.((((.....)))).)))))).....))...))))..----------..........(((((....))).))......... ( -13.80)
>DroSim_CAF1 24736 93 - 1
UCUCACGCCAUUCCCAUCAAGAAAUGCUUGCAAAAAGUUUUUCUUUUUUCCAUUUCUGUUC----------UU--UUUUUUGCCAGUCUUCUGCGCCCGCACGCA
......((...........(((((((...(.((((((.....)))))).))))))))....----------..--......(((((....))).))..))..... ( -13.00)
>DroEre_CAF1 28016 105 - 1
UCUCACGCCAUUCCCAUCAAGAAAUGCUGGCAAAAAGUUUUUCUUUUUUCCAUUUCUGUGCUUUACUUUUUUUUCUUUUUUGCCAGUCUUCUGCGCCCGCACGCA
......((...........((((..((((((((((((.............(((....)))...............)))))))))))).))))((....))..)). ( -18.69)
>consensus
UCUCACGCCAUUCCCAUCAAGAAAUGCUUGCAAAAAGUUUUUCUUUUUUCCAUUUCUGUUC__________UU__UUUUUUGCCAGUCUUCUGCGCCCGCACGCA
........................(((.(((((((((.....)))))).................................(((((....))).))..))).))) (-11.62 = -11.88 +   0.25)

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 11:40:07 2006