Locus 6585

Sequence ID	2L_DroMel_CAF1
Location	18,512,743 – 18,512,952
Length	209
Max. P	0.875079

overview

Window 8

Location	18,512,743 – 18,512,834
Length	91
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	98.90
Mean single sequence MFE	-34.73
Consensus MFE	-33.90
Energy contribution	-34.15
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.98
SVM decision value	0.77
SVM RNA-class probability	0.845854
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512743 91 + 22407834
CCAGAUCGAGACUGGGUCUGGGAAUGUCUACGGUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGAUCCCAGACUCGAGAC
(((((((.......)))))))...........((((.((((..(((((((((...((((........)))).))))))))).)))).)))) ( -35.50)
>DroSec_CAF1 33186 91 + 1
CCAGAUCGAGACUGGGUCUGGGAAUGUCUAUGGUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGAUCCCAGACUCGAGAC
(((((((.......)))))))...........((((.((((..(((((((((...((((........)))).))))))))).)))).)))) ( -35.50)
>DroSim_CAF1 31739 91 + 1
CCAGAUCGAGACUGGGUCUGGGAAUGUCUAUGGUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGAUCCCAGACUCGAGAC
(((((((.......)))))))...........((((.((((..(((((((((...((((........)))).))))))))).)))).)))) ( -35.50)
>DroYak_CAF1 33162 91 + 1
CCAGAUCGAGACUGGGUCUUGGAAUGUCUAUGGUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGAUCCCAGACUCGAGAC
.((..(((((((...)))))))..))......((((.((((..(((((((((...((((........)))).))))))))).)))).)))) ( -32.40)
>consensus
CCAGAUCGAGACUGGGUCUGGGAAUGUCUAUGGUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGAUCCCAGACUCGAGAC
(((((((.......)))))))...........((((.((((..(((((((((...((((........)))).))))))))).)))).)))) (-33.90 = -34.15 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	18,512,775 – 18,512,874
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.15
Mean single sequence MFE	-34.16
Consensus MFE	-25.35
Energy contribution	-25.67
Covariance contribution	0.32
Combinations/Pair	1.10
Mean z-score	-1.60
Structure conservation index	0.74
SVM decision value	0.07
SVM RNA-class probability	0.570273
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512775 99 + 22407834
GUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGA----UC-----------------CCAGACUCGAGACUCGUCCCACAAUAAGAUGAAACUUGUUUCCUCUCGACUCU
((((.((((..(((((((((...((((........)))).))))----))-----------------))).)))).))))(((......((((((......))))))......))).... ( -31.10)
>DroPse_CAF1 39790 120 + 1
GUAAUGGGUAAUGGGGUUUUGGGCGCUUACAUCACAGCAGGAGGCAGACCCGACAGCAAGAUGGAGUCUCGUCUCGAGACUCGUCUCACAAUGAGAUGAAACUUGUUUCCUCUCGACUCU
.....((((...((((..((((((((((.(.........).)))).).))))).((((((...((((((((...))))))))(((((.....)))))....)))))).))))...)))). ( -39.00)
>DroSec_CAF1 33218 99 + 1
GUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGA----UC-----------------CCAGACUCGAGACUCGUCCCACAAUGAGAUGAAACUUGUUUCCUCUCGACUCU
((((.((((..(((((((((...((((........)))).))))----))-----------------))).)))).))))...........(((((.((((....)))).)))))..... ( -34.80)
>DroSim_CAF1 31771 99 + 1
GUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGA----UC-----------------CCAGACUCGAGACUCGUCCCACAAUGAGAUGAAACUUGUUUCCUCUCGACUCU
((((.((((..(((((((((...((((........)))).))))----))-----------------))).)))).))))...........(((((.((((....)))).)))))..... ( -34.80)
>DroYak_CAF1 33194 99 + 1
GUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGA----UC-----------------CCAGACUCGAGACUCGUCCCACAAUAAGAAGAAACUUGUUUCCUCUCGACUCU
((((.((((..(((((((((...((((........)))).))))----))-----------------))).)))).))))(((......((((((......))))))......))).... ( -31.10)
>consensus
GUCUGGGGUAAUGGGGUCUUGGGUGCUUACAUCACAGCAGGAGA____UC_________________CCAGACUCGAGACUCGUCCCACAAUGAGAUGAAACUUGUUUCCUCUCGACUCU
(((..(((.....((((((((((((((........))).((..........................))..)))))))))))..))).....((((.((((....)))).)))))))... (-25.35 = -25.67 +   0.32)

alignment

secondary structure

dotplot

Window 0

Location	18,512,815 – 18,512,914
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.99
Mean single sequence MFE	-32.18
Consensus MFE	-23.62
Energy contribution	-24.58
Covariance contribution	0.96
Combinations/Pair	1.11
Mean z-score	-2.10
Structure conservation index	0.73
SVM decision value	0.89
SVM RNA-class probability	0.875079
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512815 99 - 22407834
AUAAAAGCCGAGUGAGGAGGCAAAUACUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUUAUUGUGGGACGAGUCUCGAGUCUGG-----------------GA----UCUC
......(((.((..(.(((.......))).)..)))))..(((.(((((((....)..((..(((......)))..))...)))))).)))..-----------------..----.... ( -31.50)
>DroPse_CAF1 39830 117 - 1
---GACCGCGAGUGGGGAGUCAAAUAUUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGAGACGAGUCUCGAGACGAGACUCCAUCUUGCUGUCGGGUCUGCCUC
---(((.(((((...((((((.........(((((.((((.(((..(((((....)...))))..))).)))).)).)))(((....)))..))))))..))))).)))(((....))). ( -42.50)
>DroSec_CAF1 33258 99 - 1
AUAAAAGCCGAGUGAGGAGGCAAAUAUUUGUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGAGUCUCGAGUCUGG-----------------GA----UCUC
......(((.((..(.(((.......))).)..)))))..(((.(((((((....)..((..(((......)))..))...)))))).)))..-----------------..----.... ( -30.60)
>DroSim_CAF1 31811 99 - 1
AUAAAAGCCGAGUGAGGAGGCAAAUAUUUGUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGAGUCUCGAGUCUGG-----------------GA----UCUC
......(((.((..(.(((.......))).)..)))))..(((.(((((((....)..((..(((......)))..))...)))))).)))..-----------------..----.... ( -30.60)
>DroYak_CAF1 33234 99 - 1
AUAAAAGCCGAGUGAGGUGGCAAAUAUUUACUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCUUCUUAUUGUGGGACGAGUCUCGAGUCUGG-----------------GA----UCUC
......((((((((((..........))))))..))))..(((.(((((((((((....))))))))).....((((....)))))).)))..-----------------..----.... ( -25.70)
>consensus
AUAAAAGCCGAGUGAGGAGGCAAAUAUUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGAGUCUCGAGUCUGG_________________GA____UCUC
......(((.(((((.(((.......))).))))))))..(((.(((((((....)..(((((((......)))))))...)))))).)))............................. (-23.62 = -24.58 +   0.96)

alignment

secondary structure

dotplot

Window 1

Location	18,512,834 – 18,512,952
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.97
Mean single sequence MFE	-25.44
Consensus MFE	-18.74
Energy contribution	-19.42
Covariance contribution	0.68
Combinations/Pair	1.11
Mean z-score	-1.77
Structure conservation index	0.74
SVM decision value	0.28
SVM RNA-class probability	0.668050
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18512834 118 - 22407834
AGCAAAAAACAAAAGUUCCCCAA--AACAACCAAGAAGAUAUAAAAGCCGAGUGAGGAGGCAAAUACUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUUAUUGUGGGACGA
..............(((((.(((--.....................(((.((..(.(((.......))).)..)))))........((((.((((....)))).)))).))).))))).. ( -25.10)
>DroPse_CAF1 39870 104 - 1
AUAAAA-UACAGAGAUUCCACAA--AAAAA-------------GACCGCGAGUGGGGAGUCAAAUAUUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGAGACGA
......-......((((((.(..--.....-------------).(((....))))))))).........(((((.((((.(((..(((((....)...))))..))).)))).)).))) ( -22.60)
>DroSec_CAF1 33277 117 - 1
AGCAAA-AACAAAAGUUCCCCAA--AACAACCAAGAAGAUAUAAAAGCCGAGUGAGGAGGCAAAUAUUUGUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGA
......-.......(((((.(((--.....................(((.((..(.(((.......))).)..)))))........((((.((((....)))).)))).))).))))).. ( -26.80)
>DroSim_CAF1 31830 117 - 1
AGCAAA-AACAAAAGUUCCCCAA--AACAACCAAGAAGAUAUAAAAGCCGAGUGAGGAGGCAAAUAUUUGUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGA
......-.......(((((.(((--.....................(((.((..(.(((.......))).)..)))))........((((.((((....)))).)))).))).))))).. ( -26.80)
>DroYak_CAF1 33253 119 - 1
AGCAAA-AACAAAGGUUCCCCAAAAAACAACCAAGAAGAUAUAAAAGCCGAGUGAGGUGGCAAAUAUUUACUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCUUCUUAUUGUGGGACGA
......-.......(((((.(((.......(((((.((((((....(((......))).....)))))).))..))).........(((((((((....))))))))).))).))))).. ( -25.90)
>consensus
AGCAAA_AACAAAAGUUCCCCAA__AACAACCAAGAAGAUAUAAAAGCCGAGUGAGGAGGCAAAUAUUUAUUGCUGGCAAAGAGUCGAGAGGAAACAAGUUUCAUCUCAUUGUGGGACGA
..............(((((.(((.......................(((.(((((.(((.......))).))))))))........((((.((((....)))).)))).))).))))).. (-18.74 = -19.42 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:54 2006