Locus 476

Sequence ID	2L_DroMel_CAF1
Location	1,386,746 – 1,386,849
Length	103
Max. P	0.987452

overview

Window 2

Location	1,386,746 – 1,386,849
Length	103
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	73.66
Mean single sequence MFE	-28.24
Consensus MFE	-11.44
Energy contribution	-13.40
Covariance contribution	1.96
Combinations/Pair	1.25
Mean z-score	-2.02
Structure conservation index	0.41
SVM decision value	1.05
SVM RNA-class probability	0.906565
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1386746 103 + 22407834
AAAGCGAUUUUGGCAACAAGCACUUGGCACCCAUUGUUGGUUUCACUUCCACGCCCCACGUUGGGCGCCACAAGCUGGGGU--UUUUUUUUCAAUGUACUCACCA
..(((...((((....))))....((((.((((.(((.((..............)).))).)))).))))...))).((((--..............)))).... ( -24.18)
>DroSec_CAF1 5226 100 + 1
AAGGCAAUUUUGGAAACAAACACUUGGCACCCAUCGUAGGUUUCAAUUCCAC-GCCCACGUUGGGCGCCACAAGUGCGGGU--UU--CUUUCAAUGUACUCACCA
...(((.....((((((...((((((((.((((.(((.(((...........-))).))).)))).))))..))))...))--))--)).....)))........ ( -31.90)
>DroSim_CAF1 5318 86 + 1
AAAGCCAUUUUGGCAACAAGCUCUUGGCACCCAUGGUG---------------CCCCAAGUUGGGCACCACAAGUGCGGGU--UU--CUUUCAAUGUACUCACCA
...(((.....)))...((((((...((((...(((((---------------(((......))))))))...))))))))--))--.................. ( -29.20)
>DroEre_CAF1 5331 101 + 1
AAAGCAAUUCUUGCAACGAGCAGCUGGCACCCAUAGUGGGCCUCAGCUUAAUGCCCCACAUUGGGCGCCACAACUGUGGCU--UU--CUUUCAAUGUACUCACCA
...(((.....)))...(((.((((((..(((.....)))..))))))....((((......))))(((((....))))).--..--...........))).... ( -32.60)
>DroYak_CAF1 5283 95 + 1
AAAGCAAUUUAUGCAACAAGC--------UCUGUGGUGGGCUUCACUUUAAUGCCCCACAGUGGGCGCCACAAAUGUGUGUUGUU--UUUUCAAUGUACUCACCA
...(((......((((((.((--------..((((((((((...........)))((.....)).)))))))...)).)))))).--.......)))........ ( -23.34)
>consensus
AAAGCAAUUUUGGCAACAAGCACUUGGCACCCAUGGUGGGCUUCACUUCAACGCCCCACGUUGGGCGCCACAAGUGCGGGU__UU__CUUUCAAUGUACUCACCA
...(((.....)))..........((((.((((..(((((..............)))))..)))).))))................................... (-11.44 = -13.40 +   1.96)

alignment

secondary structure

dotplot

Window 3

Location	1,386,746 – 1,386,849
Length	103
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	73.66
Mean single sequence MFE	-33.06
Consensus MFE	-16.14
Energy contribution	-18.42
Covariance contribution	2.28
Combinations/Pair	1.19
Mean z-score	-2.31
Structure conservation index	0.49
SVM decision value	2.08
SVM RNA-class probability	0.987452
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1386746 103 - 22407834
UGGUGAGUACAUUGAAAAAAAA--ACCCCAGCUUGUGGCGCCCAACGUGGGGCGUGGAAGUGAAACCAACAAUGGGUGCCAAGUGCUUGUUGCCAAAAUCGCUUU
((((((((((.((....))...--...........(((((((((...(((.((......))....)))....))))))))).))))))...)))).......... ( -29.90)
>DroSec_CAF1 5226 100 - 1
UGGUGAGUACAUUGAAAG--AA--ACCCGCACUUGUGGCGCCCAACGUGGGC-GUGGAAUUGAAACCUACGAUGGGUGCCAAGUGUUUGUUUCCAAAAUUGCCUU
.((..(.....(((...(--((--((..(((((..(((((((((.((((((.-............)))))).))))))))))))))..))))))))..)..)).. ( -39.22)
>DroSim_CAF1 5318 86 - 1
UGGUGAGUACAUUGAAAG--AA--ACCCGCACUUGUGGUGCCCAACUUGGGG---------------CACCAUGGGUGCCAAGAGCUUGUUGCCAAAAUGGCUUU
.((..(((.(.((....)--).--....(((((..((((((((......)))---------------)))))..)))))...).)))..))(((.....)))... ( -36.50)
>DroEre_CAF1 5331 101 - 1
UGGUGAGUACAUUGAAAG--AA--AGCCACAGUUGUGGCGCCCAAUGUGGGGCAUUAAGCUGAGGCCCACUAUGGGUGCCAGCUGCUCGUUGCAAGAAUUGCUUU
....((((..........--..--.(((((....)))))((((......))))....(((((..((((.....))))..)))))))))...(((.....)))... ( -36.90)
>DroYak_CAF1 5283 95 - 1
UGGUGAGUACAUUGAAAA--AACAACACACAUUUGUGGCGCCCACUGUGGGGCAUUAAAGUGAAGCCCACCACAGA--------GCUUGUUGCAUAAAUUGCUUU
(((((.((.((((.....--.....((((....))))..((((......)))).....))))..)).))))).(((--------((..(((.....))).))))) ( -22.80)
>consensus
UGGUGAGUACAUUGAAAG__AA__ACCCACACUUGUGGCGCCCAACGUGGGGCAUGAAAGUGAAACCCACCAUGGGUGCCAAGUGCUUGUUGCCAAAAUUGCUUU
.(((((.............................(((((((((..(((((..............)))))..)))))))))...((.....)).....))))).. (-16.14 = -18.42 +   2.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:04 2006