Locus 3120

Sequence ID	3L_DroMel_CAF1
Location	9,060,770 – 9,060,949
Length	179
Max. P	0.999879

overview

Window 3

Location	9,060,770 – 9,060,890
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.22
Mean single sequence MFE	-38.23
Consensus MFE	-24.42
Energy contribution	-26.05
Covariance contribution	1.63
Combinations/Pair	1.45
Mean z-score	-2.86
Structure conservation index	0.64
SVM decision value	4.36
SVM RNA-class probability	0.999879
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060770 120 + 23771897
UAAACGGAGGCUAUCAGCCUCCCAAUGAGUUAAAUGGAGCCUACCCGGCACCUUCUCAGUUAAACGGAGGCUACCAGCCUCCUUUAGAAGGGAAUUUAGGUUACCGACCACUUUCUCAAC
.....((((((.....))))))...((((..((.(((.(((.....)))((((((((..(((((.((((((.....)))))))))))..))))....))))......))).)).)))).. ( -43.60)
>DroSec_CAF1 6200 120 + 1
UAAACGGAGCCUACCAACCUCCUUCUCAGUUGAACGGAGGCUACAAGCCACCUUCUCAGUUUAACGAAGGCUACCAGCCUCCUGUAGAAAGAGAUUGGGGUUACCAGCCACCUUCUCAAC
.....((((.........))))......(((((..((.((((...((((.((.((((..((((....((((.....))))....))))..))))..))))))...)))).))...))))) ( -35.50)
>DroEre_CAF1 6200 120 + 1
UAAAUGGAGGCUACCAGCCACCUUCUCAGCCAAACGGAGGCUACCAGCCACCCUCUCAGCCAAACGGAGGCUAUCAGCCACCCGUGGACAGAGAUUGGGGUUACCAGCCACCAUCUCAAG
...((((.((((...((((.((.((((..(((...((.((((...((((.((.............)).))))...)))).))..)))...))))..))))))...)))).))))...... ( -41.92)
>DroYak_CAF1 6109 120 + 1
CAAACGGAGGUUAUCAGCCACCUUCUCAGUCAAGCGGAGGUUACCAGCCACCUGUAGAAAGAGAUUGGGGUUACCAGCCACCAUCUCAAGAAAAUAGUGGAUACCAGCCACCACACCAAU
.....((.((((.....((((.(((((((....((((......)).))...))).)))).(((((.(((((.....))).))))))).........)))).....)))).))........ ( -31.90)
>consensus
UAAACGGAGGCUACCAGCCACCUUCUCAGUCAAACGGAGGCUACCAGCCACCUUCUCAGUUAAACGGAGGCUACCAGCCACCUGUAGAAAGAAAUUGGGGUUACCAGCCACCAUCUCAAC
.....((.((((...((((((..((((........((.(((.....))).))........((((.((((((.....)))))).))))...))))..))))))...)))).))........ (-24.42 = -26.05 +   1.63)

alignment

secondary structure

dotplot

Window 4

Location	9,060,770 – 9,060,890
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	72.22
Mean single sequence MFE	-46.00
Consensus MFE	-27.31
Energy contribution	-28.87
Covariance contribution	1.56
Combinations/Pair	1.32
Mean z-score	-2.41
Structure conservation index	0.59
SVM decision value	2.84
SVM RNA-class probability	0.997339
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060770 120 - 23771897
GUUGAGAAAGUGGUCGGUAACCUAAAUUCCCUUCUAAAGGAGGCUGGUAGCCUCCGUUUAACUGAGAAGGUGCCGGGUAGGCUCCAUUUAACUCAUUGGGAGGCUGAUAGCCUCCGUUUA
..((((.((((((..(((.((((......((((((...((((((.....)))))).........))))))....))))..)))))))))..))))...((((((.....))))))..... ( -43.10)
>DroSec_CAF1 6200 120 - 1
GUUGAGAAGGUGGCUGGUAACCCCAAUCUCUUUCUACAGGAGGCUGGUAGCCUUCGUUAAACUGAGAAGGUGGCUUGUAGCCUCCGUUCAACUGAGAAGGAGGUUGGUAGGCUCCGUUUA
.....(((.(..(((.......(((((((((((((.((((((((((((.((((((..........)))))).)))...)))))))(.....))))))))))))))))..)))..).))). ( -46.50)
>DroEre_CAF1 6200 120 - 1
CUUGAGAUGGUGGCUGGUAACCCCAAUCUCUGUCCACGGGUGGCUGAUAGCCUCCGUUUGGCUGAGAGGGUGGCUGGUAGCCUCCGUUUGGCUGAGAAGGUGGCUGGUAGCCUCCAUUUA
....((((((.(((((.((.((((..((((.(((.(((((.(((((.(((((.((.(((.....))).)).))))).))))))))))..))).)))).)).)).)).))))).)))))). ( -57.00)
>DroYak_CAF1 6109 120 - 1
AUUGGUGUGGUGGCUGGUAUCCACUAUUUUCUUGAGAUGGUGGCUGGUAACCCCAAUCUCUUUCUACAGGUGGCUGGUAACCUCCGCUUGACUGAGAAGGUGGCUGAUAACCUCCGUUUG
...(((..(((.((..(...((((((((((...)))))))))))..)).))).((..(.((((((.(((((((..((...)).)))))))....)))))).)..))...)))........ ( -37.40)
>consensus
GUUGAGAAGGUGGCUGGUAACCCCAAUCUCCUUCUAAAGGAGGCUGGUAGCCUCCGUUUAACUGAGAAGGUGGCUGGUAGCCUCCGUUUAACUGAGAAGGAGGCUGAUAGCCUCCGUUUA
.....(((((.((.(((.....))).)).)))))....((((((((.((((((((.............((.(((.....))).)).............)))))))).))))))))..... (-27.31 = -28.87 +   1.56)

alignment

secondary structure

dotplot

Window 5

Location	9,060,810 – 9,060,916
Length	106
Sequences	4
Columns	106
Reading direction	forward
Mean pairwise identity	73.11
Mean single sequence MFE	-27.90
Consensus MFE	-15.24
Energy contribution	-16.62
Covariance contribution	1.38
Combinations/Pair	1.46
Mean z-score	-2.10
Structure conservation index	0.55
SVM decision value	1.24
SVM RNA-class probability	0.935366
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060810 106 + 23771897
CUACCCGGCACCUUCUCAGUUAAACGGAGGCUACCAGCCUCCUUUAGAAGGGAAUUUAGGUUACCGACCACUUUCUCAACAAAAUAGUGGAUAUCAGCCACCACAG
......(((((((((((..(((((.((((((.....)))))))))))..))))....))))......(((((.............)))))......)))....... ( -32.02)
>DroSec_CAF1 6240 106 + 1
CUACAAGCCACCUUCUCAGUUUAACGAAGGCUACCAGCCUCCUGUAGAAAGAGAUUGGGGUUACCAGCCACCUUCUCAACAAAAUAGUGGAUAUCAGCCAGCACAG
......((..((.((((..((((....((((.....))))....))))..))))..))((((.....((((...............)))).....)))).)).... ( -24.06)
>DroEre_CAF1 6240 106 + 1
CUACCAGCCACCCUCUCAGCCAAACGGAGGCUAUCAGCCACCCGUGGACAGAGAUUGGGGUUACCAGCCACCAUCUCAAGAAAAUAGUGGAUAUCAGCCACCACAC
.......((((.......((((...((.(((.....))).))..))).).(((((.(((((.....))).))))))).........))))................ ( -27.80)
>DroYak_CAF1 6149 106 + 1
UUACCAGCCACCUGUAGAAAGAGAUUGGGGUUACCAGCCACCAUCUCAAGAAAAUAGUGGAUACCAGCCACCACACCAAUCAACUGGUGGAUAUCAGCCACCUAUC
.............((((...(((((.(((((.....))).))))))).........((((.......((((((...........)))))).......)))))))). ( -27.74)
>consensus
CUACCAGCCACCUUCUCAGUUAAACGGAGGCUACCAGCCACCUGUAGAAAGAAAUUGGGGUUACCAGCCACCAUCUCAACAAAAUAGUGGAUAUCAGCCACCACAC
............((((...(((((.((((((.....)))))).))))).)))).....((((.....(((((.............))))).....))))....... (-15.24 = -16.62 +   1.38)

alignment

secondary structure

dotplot

Window 6

Location	9,060,850 – 9,060,949
Length	99
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	77.61
Mean single sequence MFE	-26.14
Consensus MFE	-14.87
Energy contribution	-15.50
Covariance contribution	0.63
Combinations/Pair	1.07
Mean z-score	-2.84
Structure conservation index	0.57
SVM decision value	2.43
SVM RNA-class probability	0.993803
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060850 99 + 23771897
CCUUUAGAAGGGAAUUUAGGUUACCGACCACUUUCUCAACAAAAUAGUGGAUAUCAGCCACCACAGCCAUCAACUGGUGGAUAUCAGCCACCUUUCCAA
......((((((......((((.....(((((.............))))).....)))).......(((((....)))))..........))))))... ( -21.92)
>DroSec_CAF1 6280 99 + 1
CCUGUAGAAAGAGAUUGGGGUUACCAGCCACCUUCUCAACAAAAUAGUGGAUAUCAGCCAGCACAGUCAUUAACUGGUGGAUAUCAGCCACCUUCCCAA
......(((.((((..(((((.....))).)).)))).........(((((((((.(((((............))))).)))))...)))).))).... ( -24.60)
>DroEre_CAF1 6280 99 + 1
CCCGUGGACAGAGAUUGGGGUUACCAGCCACCAUCUCAAGAAAAUAGUGGAUAUCAGCCACCACACCAACCAACUGGUGGCUACCAGCCACCCCUCCAA
....((((..(((((.(((((.....))).))))))).........((((.....((((((((...........)))))))).....))))...)))). ( -34.20)
>DroYak_CAF1 6189 99 + 1
CCAUCUCAAGAAAAUAGUGGAUACCAGCCACCACACCAAUCAACUGGUGGAUAUCAGCCACCUAUCCAAUCAACUGGUGGAUAUCAGCCACCUAUCCAA
.................((((((...((.....(((((......)))))((((((.((((..............)))).)))))).))....)))))). ( -23.84)
>consensus
CCUGUAGAAAGAAAUUGGGGUUACCAGCCACCAUCUCAACAAAAUAGUGGAUAUCAGCCACCACACCAAUCAACUGGUGGAUAUCAGCCACCUUUCCAA
..................((((.....(((((.............))))).....))))................(((((.......)))))....... (-14.87 = -15.50 +   0.63)

alignment

secondary structure

dotplot

Window 7

Location	9,060,850 – 9,060,949
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	77.61
Mean single sequence MFE	-32.33
Consensus MFE	-19.98
Energy contribution	-20.60
Covariance contribution	0.62
Combinations/Pair	1.35
Mean z-score	-1.80
Structure conservation index	0.62
SVM decision value	0.31
SVM RNA-class probability	0.684442
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9060850 99 - 23771897
UUGGAAAGGUGGCUGAUAUCCACCAGUUGAUGGCUGUGGUGGCUGAUAUCCACUAUUUUGUUGAGAAAGUGGUCGGUAACCUAAAUUCCCUUCUAAAGG
..((((((((.(((((...((((...(..(..(..(((((((.......))))))).)..)..)....))))))))).))))...)))).......... ( -27.30)
>DroSec_CAF1 6280 99 - 1
UUGGGAAGGUGGCUGAUAUCCACCAGUUAAUGACUGUGCUGGCUGAUAUCCACUAUUUUGUUGAGAAGGUGGCUGGUAACCCCAAUCUCUUUCUACAGG
(..(.(((((((..((((((..(((((..........)))))..))))))..))))))).)..)(((((.(..(((.....)))..).)))))...... ( -29.60)
>DroEre_CAF1 6280 99 - 1
UUGGAGGGGUGGCUGGUAGCCACCAGUUGGUUGGUGUGGUGGCUGAUAUCCACUAUUUUCUUGAGAUGGUGGCUGGUAACCCCAAUCUCUGUCCACGGG
.....(((((.((..((((((((((...........)))))))))....((((((((((...)))))))))))..)).))))).....(((....))). ( -39.30)
>DroYak_CAF1 6189 99 - 1
UUGGAUAGGUGGCUGAUAUCCACCAGUUGAUUGGAUAGGUGGCUGAUAUCCACCAGUUGAUUGGUGUGGUGGCUGGUAUCCACUAUUUUCUUGAGAUGG
.((((((...((((...((((((((((..(((((...((((.....))))..)))))..))))))).)))))))..))))))(((((((...))))))) ( -33.10)
>consensus
UUGGAAAGGUGGCUGAUAUCCACCAGUUGAUGGCUGUGGUGGCUGAUAUCCACUAUUUUGUUGAGAAGGUGGCUGGUAACCCCAAUCUCCUUCUAAAGG
..((((((((((.......))))).............(((.((((....(((((((((.....))))))))).)))).)))....)))))......... (-19.98 = -20.60 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:04 2006