Locus 1430

Sequence ID	2L_DroMel_CAF1
Location	3,813,402 – 3,813,553
Length	151
Max. P	0.934940

overview

Window 0

Location	3,813,402 – 3,813,514
Length	112
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	73.66
Mean single sequence MFE	-28.28
Consensus MFE	-17.41
Energy contribution	-17.17
Covariance contribution	-0.24
Combinations/Pair	1.17
Mean z-score	-1.87
Structure conservation index	0.62
SVM decision value	1.24
SVM RNA-class probability	0.934940
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3813402 112 - 22407834
CCACAGCACCAAAGCAGUUU----ACUGCUUGCUUUUGAGCACUGCUCUCCUUGCAACAACAAUCAUUUGUGUCCCUUUACAGCACUGUUCGGCUCACAGACAUCGAU---AAGUUAUC
.....(((...((((((...----.))))))......((((...))))....)))...........((((((..((...(((....)))..))..)))))).......---........ ( -23.10)
>DroSec_CAF1 2417 107 - 1
CCACAGCAAUAAAGCAGUUC----ACUGCUUGCUUUUGAGCACUGCUCUCCUUGCAACAACAACCAUUUGUGGGCCUUUACAGCACCGUUCA-----CAGACAUCGAU---AAGUUAUC
.....((((..((((((...----.))))))......((((...))))...))))...........(((((((((............)))))-----)))).......---........ ( -22.00)
>DroSim_CAF1 2412 111 - 1
CCACAGCAGUAAAGCAGUUC----UCUGCUUGCUCUUGAGCACUGCUCUCCUUGCAACAACAAUCAUUUGUGGUCCUUUACAGCACUGUUCGGUAC-AAGACAUCGAU---AAGUUAUC
((((((((((.((((((...----.))))))(((....)))))))).....(((......))).....)))))...........(((..(((((..-.....))))).---.))).... ( -25.90)
>DroEre_CAF1 2432 108 - 1
ACACAGCACUAAAGCAGUGCGCGCACUGCUUGCUUUUGCGCACUGUUAUCGGUUCAAUAGCAAUUGUUUUCGACCCUCCACUGCACUGUGAG--------CGAUAAAU---GUGUUAUC
(((((((....((((((((....))))))))((....))))....(((((((((....(((....)))...))))...(((......)))..--------.))))).)---)))).... ( -30.30)
>DroYak_CAF1 2339 111 - 1
CCACAGCACCUAAGCAGUGCACGAACUGCUUGCUUUUGCGCACUGUUAUCGCUUGAACAGCAAUAGCUUGCGACCCUUCACAGCACUGUGAA--------CGAUAAGUGCUGUGUUAUC
.((((((((.((((((((......))))))))......((((..(((((.(((.....))).))))).))))..(.((((((....))))))--------.)....))))))))..... ( -40.10)
>consensus
CCACAGCACUAAAGCAGUUC____ACUGCUUGCUUUUGAGCACUGCUCUCCUUGCAACAACAAUCAUUUGUGACCCUUUACAGCACUGUUCG______AGACAUCGAU___AAGUUAUC
....((((....((((((......))))))))))..((((((.((((............((((....))))..........)))).))))))........................... (-17.41 = -17.17 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	3,813,439 – 3,813,553
Length	114
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	77.56
Mean single sequence MFE	-32.50
Consensus MFE	-18.23
Energy contribution	-19.55
Covariance contribution	1.32
Combinations/Pair	1.28
Mean z-score	-1.76
Structure conservation index	0.56
SVM decision value	0.14
SVM RNA-class probability	0.602482
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3813439 114 + 22407834
AAAGGGACACAAAUGAUUGUUGUUGCAAGGAGAGCAGUGCUCAAAAGCAAGCAGU----AAACUGCUUUGGUGCUGUGGCGGAA-ACCCGCGGAGAUUUAAACUCCUGUCGUAUCAUUU
...(.(((((((....))).)))).).(((((.((((..(.(((.....(((((.----...)))))))))..)))).((((..-..))))...........)))))............ ( -34.30)
>DroSec_CAF1 2449 114 + 1
AAAGGCCCACAAAUGGUUGUUGUUGCAAGGAGAGCAGUGCUCAAAAGCAAGCAGU----GAACUGCUUUAUUGCUGUGGAUAAA-AACCGCGCACAUUUAAACUCCACUCGUAUCAUUU
..........((((((((((....))))(((((((((((((....)))((((((.----...)))))).))))))((((.....-..))))...........)))).......)))))) ( -30.20)
>DroSim_CAF1 2448 115 + 1
AAAGGACCACAAAUGAUUGUUGUUGCAAGGAGAGCAGUGCUCAAGAGCAAGCAGA----GAACUGCUUUACUGCUGUGGAUAAAAAACCGCGAACAUUUAAACUUCAGUCGUAUCAUUU
............(((((((..(((.....(..(((((((((....)))((((((.----...)))))).))))))((((........))))...).....)))..)))))))....... ( -29.80)
>DroEre_CAF1 2461 118 + 1
GGAGGGUCGAAAACAAUUGCUAUUGAACCGAUAACAGUGCGCAAAAGCAAGCAGUGCGCGCACUGCUUUAGUGCUGUGUAUAAA-AACCGCUAAUAUUCAAACUCCAUACUUAUCAGCU
((((.((((....((((....))))...)))).((((..(((....))((((((((....))))))))..)..)))).......-.................))))............. ( -32.10)
>DroYak_CAF1 2371 117 + 1
GAAGGGUCGCAAGCUAUUGCUGUUCAAGCGAUAACAGUGCGCAAAAGCAAGCAGUUCGUGCACUGCUUAGGUGCUGUGGUUA-A-AGCCGCGCACAUUCAAACUCCAUUCUUAUCAGUU
((((((((((.(((....)))......)))))....((((((...((((((((((......))))))....))))..(((..-.-.))))))))).........)).)))......... ( -36.10)
>consensus
AAAGGGCCACAAAUGAUUGUUGUUGCAAGGAGAGCAGUGCUCAAAAGCAAGCAGU____GAACUGCUUUAGUGCUGUGGAUAAA_AACCGCGAACAUUUAAACUCCAGUCGUAUCAUUU
...(((....(((((.((((.(((.........(((((((......))(((((((......)))))))....)))))........))).)))).)))))....)))............. (-18.23 = -19.55 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:28 2006