Locus 2538

Sequence ID	2R_DroMel_CAF1
Location	9,031,068 – 9,031,174
Length	106
Max. P	0.964259

overview

Window 7

Location	9,031,068 – 9,031,174
Length	106
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	71.09
Mean single sequence MFE	-19.77
Consensus MFE	-8.88
Energy contribution	-11.63
Covariance contribution	2.75
Combinations/Pair	1.20
Mean z-score	-2.18
Structure conservation index	0.45
SVM decision value	1.56
SVM RNA-class probability	0.964259
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9031068 106 + 20766785
UAGACAGAACCGAAAACCAAAGUUACCUGGGUUUUCGGUUCUAGACCUAUGAAAAAAAAAUUUAUUUAUUUGGACUCAUUUGAAUAUAUUCUAAAAAAUAAAAUCC
((((.(((((((((((((..((....)).)))))))))))))....................((((((..((....))..))))))...))))............. ( -24.10)
>DroPse_CAF1 7636 84 + 1
GAG------------AACAAGGGUGCCUGGUUUUUCGGUUUCACAUCAAUGAAACACA-----CUUUCUUUGGAGUUCUUUUAACAUUA----ACAA-AAAAUUUU
(((------------(((....(((.((((....))))...))).((((.((((....-----.)))).)))).)))))).........----....-........ ( -12.40)
>DroSec_CAF1 7394 102 + 1
UAGACAGAACCGAAAACCAAAGUUACCUGUGUUUUCGGUUCUAGACCUAUGAAAA-AAAA-UUAUUUAUUUGGACUCAUUUGAAUAUUUUCUAAAAA--AAAAUCC
((((.((((((((((((((........)).)))))))))))).............-....-.((((((..((....))..))))))...))))....--....... ( -22.30)
>DroSim_CAF1 6744 102 + 1
UAGACAGGACCGAAAACCAAAGUUACCUGGGUUUUCGGUUCUAGACCUAUGAAAAAAAAA-UUAUUUAUUUGGACUCAUUUGAAUAUUUUCUAAAA---AAAAUCC
((((.(((((((((((((..((....)).)))))))))))))..................-.((((((..((....))..))))))...))))...---....... ( -23.60)
>DroYak_CAF1 7380 99 + 1
UAGACAGAACCGAAAACCAAAGUUGCCUGGGUUUUCGGUUCUAUACCUAUGAAAA---AA-UUAUCUAUCUGGACUCAUUGGAAUAUUUUCUAAAAA---AAAACA
((((.(((((((((((((..((....)).)))))))))))))...((.((((...---..-..............)))).)).......))))....---...... ( -23.81)
>DroPer_CAF1 4396 84 + 1
GAG------------AACAAGGGUGCCUGGUUUUUCGGUUUCACAUCAAUGAAACACA-----CUUUCUUUGGAGUUCUUUUAACAUUA----ACAA-AAAAUUUU
(((------------(((....(((.((((....))))...))).((((.((((....-----.)))).)))).)))))).........----....-........ ( -12.40)
>consensus
UAGACAGAACCGAAAACCAAAGUUACCUGGGUUUUCGGUUCUAGACCUAUGAAAAAAAAA_UUAUUUAUUUGGACUCAUUUGAAUAUUUUCUAAAAA__AAAAUCC
.....(((((((((((((..((....)).)))))))))))))................................................................ ( -8.88 = -11.63 +   2.75)

alignment

secondary structure

dotplot

Window 8

Location	9,031,068 – 9,031,174
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	71.09
Mean single sequence MFE	-21.08
Consensus MFE	-7.45
Energy contribution	-9.28
Covariance contribution	1.84
Combinations/Pair	1.15
Mean z-score	-2.00
Structure conservation index	0.35
SVM decision value	0.43
SVM RNA-class probability	0.733163
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9031068 106 - 20766785
GGAUUUUAUUUUUUAGAAUAUAUUCAAAUGAGUCCAAAUAAAUAAAUUUUUUUUUCAUAGGUCUAGAACCGAAAACCCAGGUAACUUUGGUUUUCGGUUCUGUCUA
((((((.....(((.(((....)))))).))))))......................((((..((((((((((((((.(((...))).)))))))))))))))))) ( -26.50)
>DroPse_CAF1 7636 84 - 1
AAAAUUUU-UUGU----UAAUGUUAAAAGAACUCCAAAGAAAG-----UGUGUUUCAUUGAUGUGAAACCGAAAAACCAGGCACCCUUGUU------------CUC
....((((-(((.----....(((.....)))..)))))))..-----((.(((((((....)))))))))...(((.(((...))).)))------------... ( -10.50)
>DroSec_CAF1 7394 102 - 1
GGAUUUU--UUUUUAGAAAAUAUUCAAAUGAGUCCAAAUAAAUAA-UUUU-UUUUCAUAGGUCUAGAACCGAAAACACAGGUAACUUUGGUUUUCGGUUCUGUCUA
((((((.--..(((.(((....)))))).))))))..........-....-......((((..(((((((((((((.((((....))))))))))))))))))))) ( -26.00)
>DroSim_CAF1 6744 102 - 1
GGAUUUU---UUUUAGAAAAUAUUCAAAUGAGUCCAAAUAAAUAA-UUUUUUUUUCAUAGGUCUAGAACCGAAAACCCAGGUAACUUUGGUUUUCGGUCCUGUCUA
((((((.---.(((.(((....)))))).))))))..........-...........((((..(((.((((((((((.(((...))).)))))))))).))))))) ( -23.40)
>DroYak_CAF1 7380 99 - 1
UGUUUU---UUUUUAGAAAAUAUUCCAAUGAGUCCAGAUAGAUAA-UU---UUUUCAUAGGUAUAGAACCGAAAACCCAGGCAACUUUGGUUUUCGGUUCUGUCUA
((((((---(.....)))))))..((.(((((...((((.....)-))---).))))).)).(((((((((((((((.((....))..)))))))))))))))... ( -29.60)
>DroPer_CAF1 4396 84 - 1
AAAAUUUU-UUGU----UAAUGUUAAAAGAACUCCAAAGAAAG-----UGUGUUUCAUUGAUGUGAAACCGAAAAACCAGGCACCCUUGUU------------CUC
....((((-(((.----....(((.....)))..)))))))..-----((.(((((((....)))))))))...(((.(((...))).)))------------... ( -10.50)
>consensus
GGAUUUU__UUUUUAGAAAAUAUUCAAAUGAGUCCAAAUAAAUAA_UUUUUUUUUCAUAGGUCUAGAACCGAAAACCCAGGCAACUUUGGUUUUCGGUUCUGUCUA
...................................................................((((((((((.(((...))).))))))))))........ ( -7.45 =  -9.28 +   1.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:27 2006