Locus 2020

Sequence ID	2R_DroMel_CAF1
Location	7,598,840 – 7,598,978
Length	138
Max. P	0.995033

overview

Window 2

Location	7,598,840 – 7,598,939
Length	99
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	81.97
Mean single sequence MFE	-30.06
Consensus MFE	-20.41
Energy contribution	-20.70
Covariance contribution	0.29
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.68
SVM decision value	0.28
SVM RNA-class probability	0.666966
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7598840 99 - 20766785
AGCUCUGGAGCUCUGGAGCUCCGAACUGUGGAGCUGGGAAAACUCUGGUGAGAAUCCACAGAGCCAUAGUUUCGCAUUUGCAC----ACACGUAAUCAUCGAA
.((...((((((....))))))(((((((((..((((((...(((....)))..))).)))..))))))))).))..((((..----....))))........ ( -36.40)
>DroSec_CAF1 44407 102 - 1
AGCUCUGGAGCUCUGUAGCUCCGAACUGUGGAGCUGGGAAAACUCUGGUGUGAAUCCGCAGAGCCAUUGUUUUGCAUUUGCACA-ACACACGUAAUCAUCAAA
.(((((((((((....)))))).....(((((((..((.....))..)).....))))))))))...((((.(((....))).)-)))............... ( -31.10)
>DroSim_CAF1 45265 103 - 1
AGCUCAGGAGCUCUGUAGCUCCGAACUGCGGAGCUGGGAAAACUCUGGUGUGAAUCCGCAGAGCCAUAGUUUUGCAUUUGCACACACACACGUAAUCAUCAAA
......((((.(((.((((((((.....)))))))))))...)))).(((((.....(((((((....))))))).....))))).................. ( -32.10)
>DroEre_CAF1 43730 77 - 1
---------------------CGGACUGCGGAUCUG-GAAAACUCUGGCGAGAAUCCGCAGAGCCAUAGUUUCGCAUUUGCAC----ACAUGUAAUCAUCAAC
---------------------.((.(((((((((..-((....))..).....))))))))..))........((....))..----................ ( -19.10)
>DroYak_CAF1 45282 99 - 1
AGCUCUGGAGCUCUGGAGUUGCGGAUUGCGGAUCUGGGAAAACUCUGGUGAGAAUCCGCAGAGCCAUAGUUUCGCAUUUGCAC----ACAUGUAAUCAUCAAA
.((...((((((.(((..(((((((((.(..(((.(((....))).)))..))))))))))..))).))))))))..(((((.----...)))))........ ( -31.60)
>consensus
AGCUCUGGAGCUCUGGAGCUCCGAACUGCGGAGCUGGGAAAACUCUGGUGAGAAUCCGCAGAGCCAUAGUUUCGCAUUUGCAC____ACACGUAAUCAUCAAA
......((((((....))))))((..((((((((((((....(((((.((......))))))))).)))))))))).((((..........))))))...... (-20.41 = -20.70 +   0.29)

alignment

secondary structure

dotplot

Window 3

Location	7,598,871 – 7,598,978
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	83.93
Mean single sequence MFE	-37.34
Consensus MFE	-27.33
Energy contribution	-29.38
Covariance contribution	2.05
Combinations/Pair	1.06
Mean z-score	-3.24
Structure conservation index	0.73
SVM decision value	2.53
SVM RNA-class probability	0.995033
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7598871 107 + 20766785
UAUGGCUCUGUGGAUUCUCACCAGAGUUUUCCCAGCUCCACAGUUCGGAGCUCCAGAGCUCCAGAGCUUCACAGCUCCGGAGUCCGGAUGCAAAUGCAAAUUAGUCU
...((((((((((....))).))))))).(((..(((((.......((((((....)))))).(((((....))))).)))))..)))(((....)))......... ( -39.00)
>DroSec_CAF1 44441 107 + 1
AAUGGCUCUGCGGAUUCACACCAGAGUUUUCCCAGCUCCACAGUUCGGAGCUACAGAGCUCCAGAGCUUCAGAGCUCCGGAGUCCGGAUCAAAAUGCAAAUUAGUCU
...(((((((.(........)))))))).(((..(((((.......((((((....)))))).(((((....))))).)))))..)))................... ( -35.90)
>DroSim_CAF1 45300 107 + 1
UAUGGCUCUGCGGAUUCACACCAGAGUUUUCCCAGCUCCGCAGUUCGGAGCUACAGAGCUCCUGAGCUCCAGAGCUCCGGAGUCCGGAUCAAAAUGCAAAUUAGUCU
...(((((((.(........)))))))).(((..((((((.(((((((((((.(((.....))))))))).))))).))))))..)))................... ( -41.80)
>DroEre_CAF1 43761 82 + 1
UAUGGCUCUGCGGAUUCUCGCCAGAGUUUUC-CAGAUCCGCAGUCCG------------------------GAGCUCCGGAGUCCGGAUAAAAAUGCAAAUUAGUCU
...((((.((((((..(((....)))...))-)..(((((.(.((((------------------------(....))))).).)))))......)))....)))). ( -29.40)
>DroYak_CAF1 45313 107 + 1
UAUGGCUCUGCGGAUUCUCACCAGAGUUUUCCCAGAUCCGCAAUCCGCAACUCCAGAGCUCCAGAGCUCCAGAGCUCCGGAGUCCGGAUCAAAAUGCAAAUUAGUCU
...((.((((.(((..(((....)))...))))))).))((((((((..(((((.((((((..(....)..)))))).))))).))))).....))).......... ( -40.60)
>consensus
UAUGGCUCUGCGGAUUCUCACCAGAGUUUUCCCAGCUCCGCAGUUCGGAGCUACAGAGCUCCAGAGCUCCAGAGCUCCGGAGUCCGGAUCAAAAUGCAAAUUAGUCU
...(((((((.(((..(((....)))..))).))).((((.(.(((((((((...(((((....)))))...))))))))).).))))..............)))). (-27.33 = -29.38 +   2.05)

alignment

secondary structure

dotplot

Window 4

Location	7,598,871 – 7,598,978
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	83.93
Mean single sequence MFE	-41.20
Consensus MFE	-25.78
Energy contribution	-28.82
Covariance contribution	3.04
Combinations/Pair	1.10
Mean z-score	-3.33
Structure conservation index	0.63
SVM decision value	1.89
SVM RNA-class probability	0.981409
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7598871 107 - 20766785
AGACUAAUUUGCAUUUGCAUCCGGACUCCGGAGCUGUGAAGCUCUGGAGCUCUGGAGCUCCGAACUGUGGAGCUGGGAAAACUCUGGUGAGAAUCCACAGAGCCAUA
................((.((((((((((((((((....)))))))))).)))))))).......(((((..((((((...(((....)))..))).)))..))))) ( -46.00)
>DroSec_CAF1 44441 107 - 1
AGACUAAUUUGCAUUUUGAUCCGGACUCCGGAGCUCUGAAGCUCUGGAGCUCUGUAGCUCCGAACUGUGGAGCUGGGAAAACUCUGGUGUGAAUCCGCAGAGCCAUU
.......(((((.........((((((((((((((....)))))))))).))))((((((((.....))))))))(((..((......))...))))))))...... ( -40.60)
>DroSim_CAF1 45300 107 - 1
AGACUAAUUUGCAUUUUGAUCCGGACUCCGGAGCUCUGGAGCUCAGGAGCUCUGUAGCUCCGAACUGCGGAGCUGGGAAAACUCUGGUGUGAAUCCGCAGAGCCAUA
...................(((.((((((((....)))))).)).)))((((((((((((((.....))))))).(((..((......))...)))))))))).... ( -41.40)
>DroEre_CAF1 43761 82 - 1
AGACUAAUUUGCAUUUUUAUCCGGACUCCGGAGCUC------------------------CGGACUGCGGAUCUG-GAAAACUCUGGCGAGAAUCCGCAGAGCCAUA
..........((.......((((((((....)).))------------------------))))(((((((((..-((....))..).....)))))))).)).... ( -27.10)
>DroYak_CAF1 45313 107 - 1
AGACUAAUUUGCAUUUUGAUCCGGACUCCGGAGCUCUGGAGCUCUGGAGCUCUGGAGUUGCGGAUUGCGGAUCUGGGAAAACUCUGGUGAGAAUCCGCAGAGCCAUA
..........(((.....((((((((((((((((((..(....)..))))))))))))).))))))))((.(((((((...(((....)))..))).)))).))... ( -50.90)
>consensus
AGACUAAUUUGCAUUUUGAUCCGGACUCCGGAGCUCUGAAGCUCUGGAGCUCUGGAGCUCCGAACUGCGGAGCUGGGAAAACUCUGGUGAGAAUCCGCAGAGCCAUA
..........((.........((((((((((((((....)))))))))).))))..........(((((((((((((.....)))))).....))))))).)).... (-25.78 = -28.82 +   3.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:04 2006