Locus 4196

Sequence ID 3L_DroMel_CAF1
Location 12,258,656 – 12,258,760
Length 104
Max. P 0.500000
window6503 window6504

overview

Window 3

Location 12,258,656 – 12,258,760
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 86.61
Mean single sequence MFE -30.99
Consensus MFE -26.31
Energy contribution -27.62
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -1.34
Structure conservation index 0.85
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12258656 104 + 23771897
GUCCCUCCUCCUUUCAAAAAAAAAAAAAAAAAGAAGAAGGGAGUGAGCUGCAAAGGCGGAGUCUGCGGCGACGGGUCGCAACUGCUUCGCACGCACCACUCUCU
....(((((((((((....................)))))))).))).(((....(((((((.((((((.....))))))...)))))))..)))......... ( -33.45)
>DroSec_CAF1 12138 102 + 1
GUCCUUCCUCCUUUCCAAAAAAAAAA-A-GAAGAUGAAGGGAGUGAGCUGCAAAGGCGGCGUCUGCGGCUACGGGUCGCAACUGCUUCGCACGCACCACUCUCU
..(((((.((((((..........))-)-)..)).)))))(((((.(((((..((((((....((((((.....)))))).)))))).))).))..)))))... ( -31.80)
>DroSim_CAF1 14592 103 + 1
GUCCUUCCUCCUUUCAAAAAAAAAAA-AUAAAGAAGAAGGGAGUGAGCUGCAAAGGCGGCGUCUGCGGCGACGGGUCGCAACUGCUUCGCACGCACCACUCUCU
..(((((.((................-.....)).)))))(((((.(((((....)))))...(((((((((((.......)))..)))).)))).)))))... ( -32.30)
>DroYak_CAF1 13077 89 + 1
GUCCUUCCCCCGU------AAAAAAA-A-GA-----AAUGGAGUGAGCUCGAAAGGCGGAGUCUGCGGCGACGGGUCGCAACUGCUUUGCACGCACCACUC--U
.............------.......-.-..-----...((((((.((.(....)(((((((.((((((.....))))))...)))))))..))..)))))--) ( -26.40)
>consensus
GUCCUUCCUCCUUUCAAAAAAAAAAA_A_AAAGAAGAAGGGAGUGAGCUGCAAAGGCGGAGUCUGCGGCGACGGGUCGCAACUGCUUCGCACGCACCACUCUCU
.....................................((((((((.(.(((....(((((((.((((((.....))))))...)))))))..)))))))))))) (-26.31 = -27.62 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,258,656 – 12,258,760
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 86.61
Mean single sequence MFE -34.24
Consensus MFE -25.64
Energy contribution -28.51
Covariance contribution 2.88
Combinations/Pair 1.06
Mean z-score -1.36
Structure conservation index 0.75
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12258656 104 - 23771897
AGAGAGUGGUGCGUGCGAAGCAGUUGCGACCCGUCGCCGCAGACUCCGCCUUUGCAGCUCACUCCCUUCUUCUUUUUUUUUUUUUUUUUGAAAGGAGGAGGGAC
...((((((.((.((((((((.((.((((....)))).)).(....)).)))))))))))))))(((((((((((((............))))))))))))).. ( -39.50)
>DroSec_CAF1 12138 102 - 1
AGAGAGUGGUGCGUGCGAAGCAGUUGCGACCCGUAGCCGCAGACGCCGCCUUUGCAGCUCACUCCCUUCAUCUUC-U-UUUUUUUUUUGGAAAGGAGGAAGGAC
...((((((.((.((((((((.((((((...)))))).((....)).).)))))))))))))))(((((..((((-(-((((......)))))))))))))).. ( -37.50)
>DroSim_CAF1 14592 103 - 1
AGAGAGUGGUGCGUGCGAAGCAGUUGCGACCCGUCGCCGCAGACGCCGCCUUUGCAGCUCACUCCCUUCUUCUUUAU-UUUUUUUUUUUGAAAGGAGGAAGGAC
...((((((.((.(((((((.....(((...((((......)))).))))))))))))))))))(((((((((((..-.............))))))))))).. ( -37.76)
>DroYak_CAF1 13077 89 - 1
A--GAGUGGUGCGUGCAAAGCAGUUGCGACCCGUCGCCGCAGACUCCGCCUUUCGAGCUCACUCCAUU-----UC-U-UUUUUUU------ACGGGGGAAGGAC
.--((((((((((.((...((....))((....))))))))(.(((........))))))))))....-----((-(-((((((.------...))))))))). ( -22.20)
>consensus
AGAGAGUGGUGCGUGCGAAGCAGUUGCGACCCGUCGCCGCAGACGCCGCCUUUGCAGCUCACUCCCUUCUUCUUC_U_UUUUUUUUUUUGAAAGGAGGAAGGAC
...((((((.((.((((((((.((.((((....)))).)).(....)).)))))))))))))))(((((((((((................))))))))))).. (-25.64 = -28.51 +   2.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:33 2006