Locus 1797

Sequence ID	2L_DroMel_CAF1
Location	4,955,574 – 4,955,724
Length	150
Max. P	0.734243

overview

Window 6

Location	4,955,574 – 4,955,691
Length	117
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	84.82
Mean single sequence MFE	-46.83
Consensus MFE	-34.66
Energy contribution	-36.88
Covariance contribution	2.22
Combinations/Pair	1.09
Mean z-score	-2.17
Structure conservation index	0.74
SVM decision value	0.13
SVM RNA-class probability	0.599836
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4955574 117 - 22407834
UUCCAUUGGUUGCGGGUGCGCUGGCCAGCAGCUGGGAUUUCUUGGCCUGCAAUUUGGCCAGCGCAAUGCGCUUCUUCUCCGCUAUCUCGGAUGAACUGCAAGUGGACAUGCUGC--GAC
........(((((((.((((((((((((((((..((....))..).))))....))))))))))).((((.(((...((((......)))).))).))))..........))))--))) ( -51.60)
>DroSec_CAF1 2537 117 - 1
UUCCAUUGGUUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAACGCAAUGCGCUUCUUCUCCGCUAUCUCGGAUGAACUGCAAGUGGACAUGCUGC--GAC
........(((((((.((((.(((((((((((..((....))..).))))....)))))).)))).((((.(((...((((......)))).))).))))..........))))--))) ( -44.90)
>DroSim_CAF1 3119 117 - 1
UUCCAUUGGUUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGCUUCUUCUCCGCUAUCUCGGAUGAACUGCAAGUGGACAUGCUGC--GAC
........(((((((.((((((((((((((((..((....))..).))))....))))))))))).((((.(((...((((......)))).))).))))..........))))--))) ( -51.50)
>DroEre_CAF1 3883 117 - 1
UUCCGUUGGAUAUGGAUGCGCUGGCCAGCAGCUGGGUCUUCUUGGCCUGCAAUUUGGCCAGCGCAAUGCGCCUCUUCUCCGCUAUUUCGGAUGAACUGCAAGUGGACAUGCUGC--GAC
.(((((.....)))))((((((((((((((((..((....))..).))))....)))))))))))...(((..(...((((((....(((.....)))..))))))...)..))--).. ( -47.70)
>DroYak_CAF1 3172 117 - 1
UUCCGUUGGAUGUGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGUUUCUUCUCCGCUAUUUCGGAUGAACUGCAAGUGGACAUGCUGC--GAC
...(((.(.((((...((((((((((((((((..((....))..).))))....))))))))))).((((.(((...((((......)))).))).)))).....)))).).))--).. ( -50.60)
>DroAna_CAF1 4035 104 - 1
UUC---------------CGCCAGCUAGGAUCUGCGCCUUCUUCGCCUGCAGCUUGGCCAGUGCAAUGCGUUUCUUCUCCGCGAUUUCGAUGGCACUGCAGGCAGACAUUGUGCAUGGA
.((---------------((((.....))...(((((..(.(..((((((((....((((.((.((((((.........))).))).)).)))).))))))))..).)..))))))))) ( -34.70)
>consensus
UUCCAUUGGUUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGCUUCUUCUCCGCUAUCUCGGAUGAACUGCAAGUGGACAUGCUGC__GAC
.((((((.........((((((((((((((((..((....))..).))))....))))))))))).((((.(((...((((......)))).))).))))))))))............. (-34.66 = -36.88 +   2.22)

alignment

secondary structure

dotplot

Window 7

Location	4,955,611 – 4,955,724
Length	113
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.94
Mean single sequence MFE	-35.55
Consensus MFE	-22.27
Energy contribution	-23.83
Covariance contribution	1.56
Combinations/Pair	1.22
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	0.43
SVM RNA-class probability	0.734243
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4955611 113 + 22407834
GGAGAAGAAGCGCAUUGCGCUGGCCAAAUUGCAGGCCAAGAAAUCCCAGCUGCUGGCCAGCGCACCCGCAACCAAUGGAAAAU-CAACAACGUCUGCAACAGGUGCGACGCAAC
.........(((...(((((((((((....((((...............)))))))))))))))..)))..............-......((((.(((.....))))))).... ( -36.96)
>DroSec_CAF1 2574 113 + 1
GGAGAAGAAGCGCAUUGCGUUGGCCAAGCUGCAGGCCAAGAAGUCCCAGCUGCUGGCCAGCGCAUCCGCAACCAAUGGAAAAU-CAACAACGUCUGCUAUAGGUGCGACGCAAC
.........(((...((((((((((((((((..(((......))).)))))..)))))))))))..((((.((.((((.....-(......)....)))).)))))).)))... ( -41.90)
>DroSim_CAF1 3156 113 + 1
GGAGAAGAAGCGCAUUGCGCUGGCCAAGCUGCAGGCCAAGAAGUCCCAGCUGCUGGCCAGCGCAUCCGCAACCAAUGGAAAAU-CAACAACGUCUGCAACAGGUGCGACGCAAC
.........(((...((((((((((((((((..(((......))).)))))..)))))))))))..)))..............-......((((.(((.....))))))).... ( -43.00)
>DroEre_CAF1 3920 110 + 1
GGAGAAGAGGCGCAUUGCGCUGGCCAAAUUGCAGGCCAAGAAGACCCAGCUGCUGGCCAGCGCAUCCAUAUCCAACGGAAAAU-CA---ACGACUGCAACAGGUGCUCCGCAGC
((((....(..(((.(((((((((((....((((...............)))))))))))))))(((.........)))....-..---.....)))..).....))))..... ( -35.96)
>DroWil_CAF1 257 96 + 1
UGAAAAGAGGCGCAUUGCCUUAGCCAAACUGCAAGCCAAGAAGACCCAAUUGU------------CCACAUCU-CCGAAAAUUCCAUCUGCCGCUUCAACAGGUUCGGC-----
......(((((.....))))).(((.((((..((((..(((.(((......))------------).......-..((....))..)))...)))).....)))).)))----- ( -17.30)
>DroYak_CAF1 3209 113 + 1
GGAGAAGAAACGCAUUGCGCUGGCCAAGCUGCAGGCCAAGAAGUCCCAGCUGCUGGCCAGCGCAUCCACAUCCAACGGAAAUU-CAACAACGACUGCAACAGGUGCUCUACAAC
((((.......(((.((((((((((((((((..(((......))).)))))..)))))))))))(((.........)))....-..........)))........))))..... ( -38.16)
>consensus
GGAGAAGAAGCGCAUUGCGCUGGCCAAACUGCAGGCCAAGAAGUCCCAGCUGCUGGCCAGCGCAUCCACAACCAACGGAAAAU_CAACAACGUCUGCAACAGGUGCGACGCAAC
......(..((((..(((((((((((....((((...............))))))))))))))).............................(((...)))))))..)..... (-22.27 = -23.83 +   1.56)

alignment

secondary structure

dotplot

Window 8

Location	4,955,611 – 4,955,724
Length	113
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-40.57
Consensus MFE	-26.73
Energy contribution	-29.57
Covariance contribution	2.84
Combinations/Pair	1.23
Mean z-score	-1.41
Structure conservation index	0.66
SVM decision value	0.16
SVM RNA-class probability	0.611752
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4955611 113 - 22407834
GUUGCGUCGCACCUGUUGCAGACGUUGUUG-AUUUUCCAUUGGUUGCGGGUGCGCUGGCCAGCAGCUGGGAUUUCUUGGCCUGCAAUUUGGCCAGCGCAAUGCGCUUCUUCUCC
(((((...((((((((.((.((.(..(...-...)..).)).)).))))))))(((((((((((((..((....))..).))))....)))))))))))))............. ( -46.90)
>DroSec_CAF1 2574 113 - 1
GUUGCGUCGCACCUAUAGCAGACGUUGUUG-AUUUUCCAUUGGUUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAACGCAAUGCGCUUCUUCUCC
...((((((((((.(((((....)))))..-..........)).))))..((((.(((((((((((..((....))..).))))....)))))).))))..))))......... ( -38.82)
>DroSim_CAF1 3156 113 - 1
GUUGCGUCGCACCUGUUGCAGACGUUGUUG-AUUUUCCAUUGGUUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGCUUCUUCUCC
...((((((((.....))).))))).....-..........((..(((.(((((((((((((((((..((....))..).))))....)))))))))).)).)))..))..... ( -46.20)
>DroEre_CAF1 3920 110 - 1
GCUGCGGAGCACCUGUUGCAGUCGU---UG-AUUUUCCGUUGGAUAUGGAUGCGCUGGCCAGCAGCUGGGUCUUCUUGGCCUGCAAUUUGGCCAGCGCAAUGCGCCUCUUCUCC
.....((((.....(.((((.....---..-....(((((.....)))))((((((((((((((((..((....))..).))))....))))))))))).)))).)....)))) ( -44.50)
>DroWil_CAF1 257 96 - 1
-----GCCGAACCUGUUGAAGCGGCAGAUGGAAUUUUCGG-AGAUGUGG------------ACAAUUGGGUCUUCUUGGCUUGCAGUUUGGCUAAGGCAAUGCGCCUCUUUUCA
-----(((((((.(((..((((....((........))((-((((.(..------------......).))))))...))))))))))))))..((((.....))))....... ( -26.40)
>DroYak_CAF1 3209 113 - 1
GUUGUAGAGCACCUGUUGCAGUCGUUGUUG-AAUUUCCGUUGGAUGUGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGUUUCUUCUCC
........(((((...(.(((.((..(...-...)..))))).)...)).((((((((((((((((..((....))..).))))....))))))))))).)))........... ( -40.60)
>consensus
GUUGCGUCGCACCUGUUGCAGACGUUGUUG_AUUUUCCAUUGGAUGCGGAUGCGCUGGCCAGCAGCUGGGACUUCUUGGCCUGCAGCUUGGCCAGCGCAAUGCGCUUCUUCUCC
...((((((((.....))).)))))....................(((.(((((((((((((((((..((....))..).))))....)))))))))).)).)))......... (-26.73 = -29.57 +   2.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:35 2006