Locus 3888

Sequence ID 2R_DroMel_CAF1
Location 12,862,461 – 12,862,571
Length 110
Max. P 0.803002
window6277 window6278

overview

Window 7

Location 12,862,461 – 12,862,571
Length 110
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 94.24
Mean single sequence MFE -20.47
Consensus MFE -18.42
Energy contribution -18.53
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.12
Structure conservation index 0.90
SVM decision value 0.62
SVM RNA-class probability 0.803002
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12862461 110 + 20766785
AGGGAAAAUGCCAUGUAAAUGCUCUCAGGGCAAAAGCUGUAGCUGUAGCCGGAGCAAAA--------AAAAAGUGUAAGAAAAAUUCCUUUGCACUCAACAAAGAAGAAAUAAAUAAC
..((......)).(((...((((((...(((...(((....)))...)))))))))...--------....((((((((.........))))))))..)))................. ( -22.80)
>DroSim_CAF1 217763 111 + 1
AGGGAAAAUGCCAUGUAAAUGCUCUCAGGGCAAAAGCUGUAGCUGUAGCCGGAGAAAAA-------AAAAAAGUGUAAGAAAAAUUCCUUUGCACUCAACAAAGAAGAAAUAAAUAAC
..((......)).(((......((((..(((...(((....)))...))).))))....-------.....((((((((.........))))))))..)))................. ( -20.30)
>DroEre_CAF1 209941 118 + 1
AGGGAAAAUGCCAUGUAAAUGCUCUCAGGGCAAAAGCUGUAGCUGUAGCUGGAGAAAAAAAAAAAAAAAAAAGUGUAAGAAAAAUUCCUUUGCACUCAACAAAGAAGAAAUAAAUAAC
..((......)).(((......((((..(((...(((....)))...))).))))................((((((((.........))))))))..)))................. ( -18.30)
>consensus
AGGGAAAAUGCCAUGUAAAUGCUCUCAGGGCAAAAGCUGUAGCUGUAGCCGGAGAAAAA_______AAAAAAGUGUAAGAAAAAUUCCUUUGCACUCAACAAAGAAGAAAUAAAUAAC
..((......)).(((......((((..(((...(((....)))...))).))))................((((((((.........))))))))..)))................. (-18.42 = -18.53 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,862,461 – 12,862,571
Length 110
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 94.24
Mean single sequence MFE -20.30
Consensus MFE -17.00
Energy contribution -17.67
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.84
SVM decision value -0.05
SVM RNA-class probability 0.507635
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12862461 110 - 20766785
GUUAUUUAUUUCUUCUUUGUUGAGUGCAAAGGAAUUUUUCUUACACUUUUU--------UUUUGCUCCGGCUACAGCUACAGCUUUUGCCCUGAGAGCAUUUACAUGGCAUUUUCCCU
(((((.((....((((((((.....))))))))..................--------...(((((((((...(((....)))...)))..).)))))..)).)))))......... ( -22.30)
>DroSim_CAF1 217763 111 - 1
GUUAUUUAUUUCUUCUUUGUUGAGUGCAAAGGAAUUUUUCUUACACUUUUUU-------UUUUUCUCCGGCUACAGCUACAGCUUUUGCCCUGAGAGCAUUUACAUGGCAUUUUCCCU
..............((.(((.((((((.(((((....)))))..........-------....((((.(((...(((....)))...)))..))))))))))))).)).......... ( -21.00)
>DroEre_CAF1 209941 118 - 1
GUUAUUUAUUUCUUCUUUGUUGAGUGCAAAGGAAUUUUUCUUACACUUUUUUUUUUUUUUUUUUCUCCAGCUACAGCUACAGCUUUUGCCCUGAGAGCAUUUACAUGGCAUUUUCCCU
..............((.(((.((((((.(((((....))))).....................((((..((...(((....)))...))...))))))))))))).)).......... ( -17.60)
>consensus
GUUAUUUAUUUCUUCUUUGUUGAGUGCAAAGGAAUUUUUCUUACACUUUUUU_______UUUUUCUCCGGCUACAGCUACAGCUUUUGCCCUGAGAGCAUUUACAUGGCAUUUUCCCU
..............((.(((.((((((.(((((....))))).....................((((.(((...(((....)))...)))..))))))))))))).)).......... (-17.00 = -17.67 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:29 2006