Locus 884

Sequence ID	2R_DroMel_CAF1
Location	4,036,295 – 4,036,455
Length	160
Max. P	0.996622

overview

Window 2

Location	4,036,295 – 4,036,415
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.64
Mean single sequence MFE	-30.74
Consensus MFE	-26.19
Energy contribution	-26.43
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.76
Structure conservation index	0.85
SVM decision value	1.23
SVM RNA-class probability	0.933868
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036295 120 + 20766785
GCCUCUUUAGACCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUAAACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
((.....((((..((((.....((((((((((((....)))))......(((.....)))....)))))))...))))))))(((((((....))))).)).......)).......... ( -27.00)
>DroSec_CAF1 18960 119 + 1
GCAUCUUUAUGCCAAGUAUUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCAUGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
((((..((.(((((..(((((...((((((((((....))))).....-)))))..)))))(((((((.(........).))))))).........)).)))))..)))).......... ( -27.60)
>DroSim_CAF1 21091 119 + 1
GCAUCUUUGGGCCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUUA
....(((((((((((((.....((((((((((((....))))).....-(((.....)))....)))))))...)))...)))))..............(((.....))).))))).... ( -32.70)
>DroEre_CAF1 18089 118 + 1
GCCUCUUUAGGCCAAGUCCUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGU-UCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
.........(((((.(..((..((((((((((((....))))).....-(((.....)))....)))))))...)).-.)))))).(((..((((.((((.......)))).)))).))) ( -32.20)
>DroYak_CAF1 22183 119 + 1
GCCUCUUUGGGCCAAGUCCUUUAUGUGGUGCAUGAACACAUGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
....((((((((((.(..((..((((((((((((....))))).....-(((.....)))....)))))))...))..).)))))..............(((.....))).))))).... ( -34.20)
>consensus
GCCUCUUUAGGCCAAGUCUUUUAUGUGGUGCAUGAACACAUGCAGAUA_ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCA
.........(((((........((((((((((((....)))))......(((.....)))....))))))).........)))))...........((.(((.....))).))....... (-26.19 = -26.43 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	4,036,295 – 4,036,415
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.64
Mean single sequence MFE	-32.00
Consensus MFE	-28.79
Energy contribution	-29.03
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.06
Structure conservation index	0.90
SVM decision value	2.72
SVM RNA-class probability	0.996622
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036295 120 - 20766785
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGUUUAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGUCUAAAGAGGC
....(((((((((.....)))))............((((((...(.....)(((((((((.....)))))......((((((....)))))))))).........))))))...)))).. ( -29.40)
>DroSec_CAF1 18960 119 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACAUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAAUACUUGGCAUAAAGAUGC
....(((((((((.....))))).............((((...(((((...(((((((((.....))))))-))).((((((....)))))).........)))))))))..)))).... ( -31.00)
>DroSim_CAF1 21091 119 - 1
UAAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGCCCAAAGAUGC
....(((((((((.....)))))............((((((..........(((((((((.....))))))-))).((((((....)))))).............)))))).)))).... ( -31.80)
>DroEre_CAF1 18089 118 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGA-ACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAGGACUUGGCCUAAAGAGGC
....(((((((((.....)))))............((((((.-.((.....(((((((((.....))))).-....((((((....)))))))))).....))..))))))...)))).. ( -34.10)
>DroYak_CAF1 22183 119 - 1
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCAUGUGUUCAUGCACCACAUAAAGGACUUGGCCCAAAGAGGC
....(((((((((.....)))))............((((((...((.....(((((((((.....))))).-....((((((....))))))))))....))...))))))...)))).. ( -33.70)
>consensus
UGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU_UAUCUGCAUGUGUUCAUGCACCACAUAAAAGACUUGGCCUAAAGAGGC
....(((((((((.....)))))............((((((..........(((((((((.....)))))......((((((....)))))))))).........)))))).)))).... (-28.79 = -29.03 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	4,036,335 – 4,036,455
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.49
Mean single sequence MFE	-31.44
Consensus MFE	-30.36
Energy contribution	-30.20
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.20
Structure conservation index	0.97
SVM decision value	0.38
SVM RNA-class probability	0.714400
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036335 120 + 20766785
UGCAGAUAAACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGUAAAAUUCAA
.((((.....((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -30.90)
>DroSec_CAF1 19000 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCAUGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((...-.((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -31.60)
>DroSim_CAF1 21131 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUUAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
........-.((.(((((.(((((((((.(........).))))))).........((.(((.....))).)).....)).)))))((((.(.(((.....))))))))))......... ( -31.10)
>DroEre_CAF1 18129 117 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGU-UCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGA-AAUUCAA
.((((...-.((.(((.(((.(((((((.(.......-.)))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))....-....... ( -32.00)
>DroYak_CAF1 22223 119 + 1
UGCAGAUA-ACCAUUCAGGUAAUGGCCACGUUACAGUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((...-.((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ ( -31.60)
>consensus
UGCAGAUA_ACCAUUCAGGUAAUGGCCACGUUACACUUUCUGGCCAUGAUUUUUUAUGCGCAAAUUAUGCACAAAGUUCAGCUGAGCGCAAGACCCGAAAAGGGCUGCGGGAAAAUUCAA
.((((.....((.(((.(((.(((((((.(........).))))))).........((((((.....))).....((((....)))))))..))).)))..)).))))............ (-30.36 = -30.20 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	4,036,335 – 4,036,455
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.49
Mean single sequence MFE	-32.16
Consensus MFE	-31.38
Energy contribution	-31.38
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.98
SVM decision value	1.31
SVM RNA-class probability	0.940562
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4036335 120 - 20766785
UUGAAUUUUACCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGUUUAUCUGCA
...........((((((((.....))))..))))..(((.((((((.((((((.....)))))).........(((((((............))))))).........)))))).))).. ( -32.00)
>DroSec_CAF1 19000 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACAUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -32.80)
>DroSim_CAF1 21131 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUAAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -31.90)
>DroEre_CAF1 18129 117 - 1
UUGAAUU-UCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGA-ACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
.......-....((((.((..(((((((...((.....)).......((((((.....)))))).........((((((((.-.......).))))))).))))))).)).-...)))). ( -32.20)
>DroYak_CAF1 22223 119 - 1
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAACUGUAACGUGGCCAUUACCUGAAUGGU-UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).-...)))). ( -31.90)
>consensus
UUGAAUUUUCCCGCAGCCCUUUUCGGGUCUUGCGCUCAGCUGAACUUUGUGCAUAAUUUGCGCAUAAAAAAUCAUGGCCAGAAAGUGUAACGUGGCCAUUACCUGAAUGGU_UAUCUGCA
............((((.((..(((((((...((.....)).......((((((.....)))))).........(((((((............))))))).))))))).)).....)))). (-31.38 = -31.38 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:04 2006