Locus 1129

Sequence ID	3L_DroMel_CAF1
Location	3,293,715 – 3,293,827
Length	112
Max. P	0.987575

overview

Window 7

Location	3,293,715 – 3,293,827
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.97
Mean single sequence MFE	-31.48
Consensus MFE	-24.66
Energy contribution	-25.46
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.91
Structure conservation index	0.78
SVM decision value	2.08
SVM RNA-class probability	0.987575
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3293715 112 + 23771897
UCUCAGUAUCUUUUUU-UUUUGUGCAAUAACAAUUUCAGAGCUUGGC-------AGGCUAUUUGUUGACUGCAUAAAAAAAGCAGUUGAAUGAACUGAGAACGAGCUUUGAUUGAUAUUU
....((((((......-..((((......))))..((((((((((.(-------((..(((((...((((((.........)))))))))))..)))....))))))))))..)))))). ( -31.20)
>DroSec_CAF1 23345 118 + 1
UCUCAGUAUCUUUUUUGUUUUGUGCAAUAACAAUUUCAGAGCUUGGCACAUUGCAGUCUAUUUGUUGACUGCAUAAA--AAGCAGUUGAAUGAACUGAGAACGAGCUUUGAUUGAUAUUU
....((((((.........((((......))))..((((((((((......(((((((........)))))))....--...(((((.....)))))....))))))))))..)))))). ( -33.70)
>DroSim_CAF1 24257 116 + 1
UCUCAGUAUCUUUUU---UUUGUGCAAUAACAAUUUCAGAGCUUGGCACAUUGCAGUCUAUUUGUUGACUGCAUAAA-AAAGCAGUUGAAUGAACUGAGAACGAGCUUUGAUUGAUAUUU
....((((((.....---.((((......))))..((((((((((......(((((((........)))))))....-....(((((.....)))))....))))))))))..)))))). ( -33.70)
>DroEre_CAF1 25494 115 + 1
UCUCAGUAUCUUUU----UUUGUGCAAUAACAAUUUCAGAGCUUGGCACAUUGCAAGCUAUUUGUUGACUGCAUAAA-AAAGCAGUUGAAUGAACUGAGAACGAGCUUUGAUUGAUAUUU
(((((((...((((----((((((((.((((((......((((((........))))))..))))))..))))))))-))))((......)).))))))).................... ( -29.70)
>DroYak_CAF1 26113 115 + 1
UCUCAGUAUCUUUU----UUUGUGCAAUAACAAUUUCCGAGCUUGGCACAUUGCAGGCUAUUUGUUGACUGCAUAAA-GAGGCAGUUGAAUGAACUGAGAACGAACUUUGAUUGAUAUUU
(((((((...((((----((((((((.((((((......((((((........))))))..))))))..))))))))-))))((......)).))))))).................... ( -29.10)
>consensus
UCUCAGUAUCUUUUU___UUUGUGCAAUAACAAUUUCAGAGCUUGGCACAUUGCAGGCUAUUUGUUGACUGCAUAAA_AAAGCAGUUGAAUGAACUGAGAACGAGCUUUGAUUGAUAUUU
....((((((.........((((......))))..((((((((((((.....))..........(..(((((.........)))))..)............))))))))))..)))))). (-24.66 = -25.46 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	3,293,715 – 3,293,827
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.97
Mean single sequence MFE	-24.35
Consensus MFE	-18.86
Energy contribution	-19.46
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.54
Structure conservation index	0.77
SVM decision value	1.50
SVM RNA-class probability	0.959173
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3293715 112 - 23771897
AAAUAUCAAUCAAAGCUCGUUCUCAGUUCAUUCAACUGCUUUUUUUAUGCAGUCAACAAAUAGCCU-------GCCAAGCUCUGAAAUUGUUAUUGCACAAAA-AAAAAAGAUACUGAGA
....................(((((((........((..(((((((.((((((.(((((..(((..-------.....)))......))))))))))).))))-)))..))..))))))) ( -19.80)
>DroSec_CAF1 23345 118 - 1
AAAUAUCAAUCAAAGCUCGUUCUCAGUUCAUUCAACUGCUU--UUUAUGCAGUCAACAAAUAGACUGCAAUGUGCCAAGCUCUGAAAUUGUUAUUGCACAAAACAAAAAAGAUACUGAGA
....................(((((((...........(((--(((.(((((((........))))))).(((((..(((.........)))...))))).....))))))..))))))) ( -26.82)
>DroSim_CAF1 24257 116 - 1
AAAUAUCAAUCAAAGCUCGUUCUCAGUUCAUUCAACUGCUUU-UUUAUGCAGUCAACAAAUAGACUGCAAUGUGCCAAGCUCUGAAAUUGUUAUUGCACAAA---AAAAAGAUACUGAGA
....................(((((((...........((((-(((.(((((((........))))))).(((((..(((.........)))...))))).)---))))))..))))))) ( -27.72)
>DroEre_CAF1 25494 115 - 1
AAAUAUCAAUCAAAGCUCGUUCUCAGUUCAUUCAACUGCUUU-UUUAUGCAGUCAACAAAUAGCUUGCAAUGUGCCAAGCUCUGAAAUUGUUAUUGCACAAA----AAAAGAUACUGAGA
....................(((((((...........((((-(((.((((((.(((((..(((((((.....).))))))......)))))))))))..))----)))))..))))))) ( -25.22)
>DroYak_CAF1 26113 115 - 1
AAAUAUCAAUCAAAGUUCGUUCUCAGUUCAUUCAACUGCCUC-UUUAUGCAGUCAACAAAUAGCCUGCAAUGUGCCAAGCUCGGAAAUUGUUAUUGCACAAA----AAAAGAUACUGAGA
....................(((((((((.....(((((...-.....))))).........((..(((((...((......))..)))))....)).....----....)).))))))) ( -22.20)
>consensus
AAAUAUCAAUCAAAGCUCGUUCUCAGUUCAUUCAACUGCUUU_UUUAUGCAGUCAACAAAUAGCCUGCAAUGUGCCAAGCUCUGAAAUUGUUAUUGCACAAA___AAAAAGAUACUGAGA
....................(((((((((.....(((((.........))))).................(((((..(((.........)))...)))))..........)).))))))) (-18.86 = -19.46 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:53 2006