Locus 891

Sequence ID	2L_DroMel_CAF1
Location	2,539,082 – 2,539,239
Length	157
Max. P	0.612021

overview

Window 8

Location	2,539,082 – 2,539,186
Length	104
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	95.97
Mean single sequence MFE	-24.67
Consensus MFE	-22.23
Energy contribution	-22.90
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.13
Structure conservation index	0.90
SVM decision value	0.15
SVM RNA-class probability	0.608373
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2539082 104 + 22407834
AUCGAAUCGAACUGCA-AAUCUCAAUGCUGCAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAGC
................-.........(((((..((((((...((((..........(((.....))).((((....))))......)))).))))))...))))) ( -25.90)
>DroSec_CAF1 118650 104 + 1
AUCGAAUCGAACUGCA-AAUCUCAAUGCUGCAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAGC
................-.........(((((..((((((...((((..........(((.....))).((((....))))......)))).))))))...))))) ( -25.90)
>DroSim_CAF1 121733 104 + 1
AUCGAAUCGAACUGCA-AAUCUCAAUGCUGCAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAGC
................-.........(((((..((((((...((((..........(((.....))).((((....))))......)))).))))))...))))) ( -25.90)
>DroEre_CAF1 121880 104 + 1
AUCGAAUCGAACUGCA-AAUCUCAAUGCUGCAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAUC
...((..((((.((((-...........)))).))))...))(((..(((.....)))....(((((...))))).)))......((((((.......)))))). ( -23.90)
>DroYak_CAF1 122279 104 + 1
AUCGAAUCGAACUGCA-AAUCUCAAUGCUGCAAAUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAUC
...((..(((..((((-...........))))..)))...))(((..(((.....)))....(((((...))))).)))......((((((.......)))))). ( -22.10)
>DroAna_CAF1 154583 99 + 1
AUCGAAG------GCACAAUCUCACUGCUACAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAGC
.......------...........((((((...((((((...((((..........(((.....))).((((....))))......)))).)))))).)))))). ( -24.30)
>consensus
AUCGAAUCGAACUGCA_AAUCUCAAUGCUGCAAUUCGUGCUCGGCAAGCAAACAUUGCAUAAAUUGCUUGGCAAUGGCCACUAAAAUGCCACAUGGAAUGGCAGC
..........................(((((..((((((...((((..........(((.....))).((((....))))......)))).))))))...))))) (-22.23 = -22.90 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	2,539,106 – 2,539,222
Length	116
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.50
Mean single sequence MFE	-34.73
Consensus MFE	-23.23
Energy contribution	-23.71
Covariance contribution	0.47
Combinations/Pair	1.12
Mean z-score	-1.58
Structure conservation index	0.67
SVM decision value	0.16
SVM RNA-class probability	0.612021
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2539106 116 - 22407834
---GGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAAUUGCAGCA
---..................((((((((((......((((..(........)..)))).....))))))))))...((((((..(((...((......))...)))..)))))).... ( -37.50)
>DroPse_CAF1 151860 100 - 1
-------------------UGGGGAAAGCCAAGACUAGUGUUGCCAUUCCAUGUGGCAUUUUAUUGGCCAUUGCCAGGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAACGCCAGCU
-------------------(((.(...((((((((....)))(((((.....)))))......)))))...(((..(((((.....(((.....))))))))..)))....).)))... ( -29.50)
>DroEre_CAF1 121904 119 - 1
UAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGAUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAAUUGCAGCA
(((......))).........((((((((((........((((((((.....))))))))....))))))))))...((((((..(((...((......))...)))..)))))).... ( -40.40)
>DroYak_CAF1 122303 119 - 1
UAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGAUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAUUUGCAGCA
(((......)))..(((....((((((((((........((((((((.....))))))))....))))))))))(((((((............)))))))))).(((.....))).... ( -39.00)
>DroAna_CAF1 154602 112 - 1
UAUGGA-------AUGGGUAAGAGAUGUCCCUGAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAAUUGUAGCA
((((((-------(((((((...(((........))).)))..))))))))))..((.......((((....)))).((((((..(((...((......))...)))..)))))).)). ( -32.50)
>DroPer_CAF1 156562 100 - 1
-------------------UGGGGAAAGCCAAGACUAGUGUUGCCAUUCCAUGUGGCAUUUUAUUGGCCAUUGCCAGGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAACGCCAGCU
-------------------(((.(...((((((((....)))(((((.....)))))......)))))...(((..(((((.....(((.....))))))))..)))....).)))... ( -29.50)
>consensus
___GGA_______AUGGAAAAGCGAUGGCCAAAAGUCGUGAUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGCAAUUUAUGCAAUGUUUGCUUGCCGAGCACGAAUUGCAGCA
.....................((((((((((..........((((((.....))))))......))))))))(((((((((............)))))))....)).......)).... (-23.23 = -23.71 +   0.47)

alignment

secondary structure

dotplot

Window 0

Location	2,539,146 – 2,539,239
Length	93
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.51
Mean single sequence MFE	-30.13
Consensus MFE	-21.61
Energy contribution	-22.11
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.24
Structure conservation index	0.72
SVM decision value	-0.03
SVM RNA-class probability	0.520635
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2539146 93 - 22407834
AAGGAGAGG-----------GAGGGCAG--------------GGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
.........-----------...(((((--------------((...((((((......(((.(((((.....))))))))(((((.....)))))..))))))..)).))))).... ( -28.30)
>DroSec_CAF1 118714 107 - 1
AAGGAGAGG-----------GAGGGCAGGGAAAGCUGGGCAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
.........-----------.............(((.(((((((...((((((......(((.(((((.....))))))))(((((.....)))))..))))))..)).))))).))) ( -31.20)
>DroSim_CAF1 121797 107 - 1
AAGGAGAGG-----------GAGGGCAGGGAAAGCUGGGCAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
.........-----------.............(((.(((((((...((((((......(((.(((((.....))))))))(((((.....)))))..))))))..)).))))).))) ( -31.20)
>DroEre_CAF1 121944 107 - 1
AAGGAGAUG-----------GAGGGCGGGGAAAACUGGGUAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGAUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
.........-----------....((..(.....(((..(((......)))..)))....((((((((((........((((((((.....))))))))....)))))))))))..)) ( -31.80)
>DroYak_CAF1 122343 118 - 1
AAGCAGUGGGGAGGGGAGGGAAGGGCAGGAAAAUCGGGGUAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGAUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
..((.............................((.(..(((......)))..).))...((((((((((........((((((((.....))))))))....))))))))))...)) ( -32.20)
>DroAna_CAF1 154642 100 - 1
GAGAAAACA-----------UAGAGCGUCUAAAUCGGGAUAUGGA-------AUGGGUAAGAGAUGUCCCUGAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
.........-----------....((..(((((..(..(((((((-------(((((((...(((........))).)))..)))))))))))..)..)))))((((....)))).)) ( -26.10)
>consensus
AAGGAGAGG___________GAGGGCAGGGAAAGCUGGGUAGGGAAAACUGGAUGGAAAAGCGAUGGCCAAAAGUCGUGCUGCCAUUCCAUGUGGCAUUUUAGUGGCCAUUGCCAAGC
............................................................((((((((((..........((((((.....))))))......))))))))))..... (-21.61 = -22.11 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:04 2006