Locus 2454

Sequence ID	X_DroMel_CAF1
Location	6,568,431 – 6,568,601
Length	170
Max. P	0.995564

overview

Window 6

Location	6,568,431 – 6,568,546
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.33
Mean single sequence MFE	-32.80
Consensus MFE	-25.01
Energy contribution	-24.97
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.56
Structure conservation index	0.76
SVM decision value	-0.04
SVM RNA-class probability	0.515412
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6568431 115 - 22224390
CAUGCAGCCAUGUAUCAUCAUCGAUCGCUGA-----UCGAUCUGUGGAUCGAGUGACACACGGGCCCGGACCCGGGGGCAAGGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
..(((..((.(((.((((..((((((((.((-----....)).)).)))))))))).))).)).((((....)))).))).(.(((((.((((.............))))))))).)... ( -30.42)
>DroSec_CAF1 13352 114 - 1
CAUGCAGCCAUGGAUCAUCAUCGAUCGCUCA-----UCGAUCUGUGGAUCGAGUGACACACGGGCCUGGACCCGG-GGCAAGGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
((((....))))((((..(((.(((((....-----.))))).)))))))(((((((((...(.((((....)))-).)...))))).))))......(((......))).......... ( -30.00)
>DroSim_CAF1 23908 114 - 1
CAUGCAGCCAUGGAUCAUCAUCGAUCGCUCA-----UCGAUCUGUGGAUCGAGUGACACACGGGCCUGGACCCGG-GGCAAGGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
((((....))))((((..(((.(((((....-----.))))).)))))))(((((((((...(.((((....)))-).)...))))).))))......(((......))).......... ( -30.00)
>DroEre_CAF1 13057 111 - 1
CAUGCAGCCAUGGAUCAUUAU---UCAGUGA-----UCGAUCUGUGGAUCGAGUGACACACGGGCCCGGACCCGG-GGCAAGGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
((((...((((((((((((((---...))))-----).)))))))))...(((((((((...(.((((....)))-).)...))))).))))............))))............ ( -33.60)
>DroYak_CAF1 22938 116 - 1
CAUGCAGCCAUGGAUCAUCGU---UCGAUGAAUCUGUGGAUCUGUGGAUUGAGUGACACACGGGCCCGGACCCGG-GGCAAAGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
(((((((((((((((((((..---..)))).))))))))..)))).(((((((((((((...(.((((....)))-).)...))))).)))))))).........)))............ ( -40.00)
>consensus
CAUGCAGCCAUGGAUCAUCAUCGAUCGCUGA_____UCGAUCUGUGGAUCGAGUGACACACGGGCCCGGACCCGG_GGCAAGGUGUUAAUUCAAUUACUUCUAUUAUGAAUAACAACAAA
((((...(((((((((......................)))))))))...(((((((((...(.((((....))).).)...))))).))))............))))............ (-25.01 = -24.97 +  -0.04)

alignment

secondary structure

dotplot

Window 7

Location	6,568,471 – 6,568,574
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.84
Mean single sequence MFE	-38.68
Consensus MFE	-27.46
Energy contribution	-28.98
Covariance contribution	1.52
Combinations/Pair	1.16
Mean z-score	-1.71
Structure conservation index	0.71
SVM decision value	0.22
SVM RNA-class probability	0.642011
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6568471 103 + 22224390
UGCCCCCGGGUCCGGGCCCGUGUGUCACUCGAUCCACAGAUCGA-----UCAGCGAUCGAUGAUGAUACAUGGCUGCAUGGAGCGGUGGUAUCACCACAUCGAUUGCC------------
.((.(.(((((....))))).).))...((((((....))))))-----...((((((((((.((((((...(((((.....))))).))))))...)))))))))).------------ ( -42.50)
>DroSec_CAF1 13392 102 + 1
UGCC-CCGGGUCCAGGCCCGUGUGUCACUCGAUCCACAGAUCGA-----UGAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUGGUAUCACCACAUCGAUUGCC------------
....-.(((((....)))))....(((.((((((....))))))-----)))((((((((((....((((((....))))))..((((....)))).)))))))))).------------ ( -45.10)
>DroSim_CAF1 23948 102 + 1
UGCC-CCGGGUCCAGGCCCGUGUGUCACUCGAUCCACAGAUCGA-----UGAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUAAUAUCACCACAUCGAUUGCC------------
....-.(((((....)))))....(((.((((((....))))))-----)))((((((((((....((((((....))))))..(((......))).)))))))))).------------ ( -42.30)
>DroEre_CAF1 13097 111 + 1
UGCC-CCGGGUCCGGGCCCGUGUGUCACUCGAUCCACAGAUCGA-----UCACUGA---AUAAUGAUCCAUGGCUGCAUGGAGCAGCAGUAUCACCUCAUCGAUUGACUAUUUUUGAAUG
....-.(((((....)))))...((((.((((((....))))((-----(.((((.---....((.((((((....)))))).)).)))))))........)).))))............ ( -32.50)
>DroYak_CAF1 22978 116 + 1
UGCC-CCGGGUCCGGGCCCGUGUGUCACUCAAUCCACAGAUCCACAGAUUCAUCGA---ACGAUGAUCCAUGGCUGCAUGGAGCGCUAGUAUCACCUCAUCGAUUGGCUAUUAUUGAAUG
.(((-.(((((....))))).(((..(((...(((((((..(((..(((.((((..---..)))))))..))))))..)))).....)))..)))..........)))............ ( -31.00)
>consensus
UGCC_CCGGGUCCGGGCCCGUGUGUCACUCGAUCCACAGAUCGA_____UCAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUAGUAUCACCACAUCGAUUGCC____________
......(((((....)))))........((((((....))))))........((((((((((.((((..((.(((((.....))))).))))))...))))))))))............. (-27.46 = -28.98 +   1.52)

alignment

secondary structure

dotplot

Window 8

Location	6,568,511 – 6,568,601
Length	90
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	77.40
Mean single sequence MFE	-29.85
Consensus MFE	-20.09
Energy contribution	-19.90
Covariance contribution	-0.19
Combinations/Pair	1.24
Mean z-score	-2.37
Structure conservation index	0.67
SVM decision value	2.22
SVM RNA-class probability	0.990587
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6568511 90 + 22224390
UCGAUCAGCGAUCGAUGAUGAUACAUGGCUGCAUGGAGCGGUGGUAUCACCACAUCGAUUGCC-------------------------UAUUGUUAUGGCUUAAUUUUAGUUGAA
....(((((((((((((.((((((...(((((.....))))).))))))...))))))))(((-------------------------.........))).........))))). ( -31.00)
>DroSec_CAF1 13431 90 + 1
UCGAUGAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUGGUAUCACCACAUCGAUUGCC-------------------------CAUUGUUGUGGCUUAAUUUUAGUUGGA
.(((((.((((((((((....((((((....))))))..((((....)))).)))))))))).-------------------------)))))....((((.......))))... ( -33.90)
>DroSim_CAF1 23987 90 + 1
UCGAUGAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUAAUAUCACCACAUCGAUUGCC-------------------------CAUUGUUGUGGCUUAAUUUUAGUUGGA
.(((((.((((((((((....((((((....))))))..(((......))).)))))))))).-------------------------)))))....((((.......))))... ( -31.10)
>DroEre_CAF1 13136 112 + 1
UCGAUCACUGA---AUAAUGAUCCAUGGCUGCAUGGAGCAGCAGUAUCACCUCAUCGAUUGACUAUUUUUGAAUGGCUCUCGUUUGCUUAUUGUUAUGACUUCAAUUUAGUUGGA
..(((.((((.---....((.((((((....)))))).)).)))))))..........(..((((...(((((.(....((((..((.....)).))))))))))..))))..). ( -23.40)
>consensus
UCGAUCAGCGAUCGAUGAUGAUCCAUGGCUGCAUGGAGCGGUAGUAUCACCACAUCGAUUGCC_________________________CAUUGUUAUGGCUUAAUUUUAGUUGGA
(((((..((((((((((.((((..((.(((((.....))))).))))))...))))))))))..........................(((....)))...........))))). (-20.09 = -19.90 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	6,568,511 – 6,568,601
Length	90
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	77.40
Mean single sequence MFE	-24.40
Consensus MFE	-16.41
Energy contribution	-16.48
Covariance contribution	0.06
Combinations/Pair	1.24
Mean z-score	-2.52
Structure conservation index	0.67
SVM decision value	2.59
SVM RNA-class probability	0.995564
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6568511 90 - 22224390
UUCAACUAAAAUUAAGCCAUAACAAUA-------------------------GGCAAUCGAUGUGGUGAUACCACCGCUCCAUGCAGCCAUGUAUCAUCAUCGAUCGCUGAUCGA
...........................-------------------------(((.(((((((..(((((((....(((......)))...)))))))))))))).)))...... ( -21.10)
>DroSec_CAF1 13431 90 - 1
UCCAACUAAAAUUAAGCCACAACAAUG-------------------------GGCAAUCGAUGUGGUGAUACCACCGCUCCAUGCAGCCAUGGAUCAUCAUCGAUCGCUCAUCGA
......................(.(((-------------------------(((.((((((((((((....))))))((((((....)))))).....)))))).)))))).). ( -29.80)
>DroSim_CAF1 23987 90 - 1
UCCAACUAAAAUUAAGCCACAACAAUG-------------------------GGCAAUCGAUGUGGUGAUAUUACCGCUCCAUGCAGCCAUGGAUCAUCAUCGAUCGCUCAUCGA
......................(.(((-------------------------(((.((((((((((((....))))))((((((....)))))).....)))))).)))))).). ( -27.50)
>DroEre_CAF1 13136 112 - 1
UCCAACUAAAUUGAAGUCAUAACAAUAAGCAAACGAGAGCCAUUCAAAAAUAGUCAAUCGAUGAGGUGAUACUGCUGCUCCAUGCAGCCAUGGAUCAUUAU---UCAGUGAUCGA
....((((..(((((((....)).....((........))..)))))...))))(.((((.(((((((((...(((((.....))))).....)))))..)---))).)))).). ( -19.20)
>consensus
UCCAACUAAAAUUAAGCCACAACAAUA_________________________GGCAAUCGAUGUGGUGAUACCACCGCUCCAUGCAGCCAUGGAUCAUCAUCGAUCGCUCAUCGA
....................................................(((.(((((((.((((....))))(.((((((....)))))).)..))))))).)))...... (-16.41 = -16.48 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:00 2006