Locus 6059

Sequence ID	2R_DroMel_CAF1
Location	19,063,842 – 19,063,974
Length	132
Max. P	0.996167

overview

Window 8

Location	19,063,842 – 19,063,941
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	82.50
Mean single sequence MFE	-26.90
Consensus MFE	-17.60
Energy contribution	-18.80
Covariance contribution	1.20
Combinations/Pair	1.15
Mean z-score	-2.35
Structure conservation index	0.65
SVM decision value	1.10
SVM RNA-class probability	0.915275
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19063842 99 + 20766785
GUUCGUUGCUGGUUCCGGUUCAAGUUCCAUUUCUUCGCCGCAACUACAGUGCCUAUCGGUUGCGGCGAAUUGCAAUUUUAAAAACCAAUUUUGUUGAAA
....((((((((..(........)..)))....((((((((((((............))))))))))))..)))))....................... ( -25.10)
>DroSec_CAF1 6327 99 + 1
GUUCGUUGCUGGUUCCGGUUCCAGUUCCAUUUCUUCGCCGCAACUACAGUUCCUAUCGAUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUAAAA
.((((..(((((........)))))..)(((((((((((((((................))))))))))..)))))..))).................. ( -24.99)
>DroSim_CAF1 6221 99 + 1
GUUCGUUGCUGGUUCCGGUUCCAGUUCCAUUUCUUCGCCGCAACUACAGUUCCUAUCGGUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUGAAA
.((((..(((((........)))))..)(((((((((((((((((............))))))))))))..)))))..))).................. ( -29.80)
>DroEre_CAF1 6274 92 + 1
AUUCGAUGCCGGUUCCGGCUCACGA------UCUUCGCCGCAACUACAGUGUCUAUCGGUUCCGGCGAAUUGGAGUUUUAAUAAC-UAUUUUACUGAAA
.(((((.((((....)))))).(((------(..((((((.((((............)))).)))))))))).((((.....)))-)........))). ( -24.10)
>DroYak_CAF1 6626 86 + 1
AUUCGGAGCCGGUU------CAAGU------UCUUCGCCGCAAAUACGGUGUCUAUCGGUUGCGGCGAAUUGGAAUUUGAAAAAC-AAUUUUAUUGAAA
..(((....)))((------(((((------((((((((((((...((((....)))).)))))))))...))))))))))....-............. ( -30.50)
>consensus
GUUCGUUGCUGGUUCCGGUUCAAGUUCCAUUUCUUCGCCGCAACUACAGUGCCUAUCGGUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUGAAA
.((((..((((....))))..............((((((((((((............)))))))))))).))))......................... (-17.60 = -18.80 +   1.20)

alignment

secondary structure

dotplot

Window 9

Location	19,063,842 – 19,063,941
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	82.50
Mean single sequence MFE	-26.80
Consensus MFE	-18.10
Energy contribution	-20.11
Covariance contribution	2.01
Combinations/Pair	1.09
Mean z-score	-2.60
Structure conservation index	0.68
SVM decision value	1.59
SVM RNA-class probability	0.966309
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19063842 99 - 20766785
UUUCAACAAAAUUGGUUUUUAAAAUUGCAAUUCGCCGCAACCGAUAGGCACUGUAGUUGCGGCGAAGAAAUGGAACUUGAACCGGAACCAGCAACGAAC
...........((((((((...........(((((((((((..((((...)))).))))))))))).....((........))))))))))........ ( -27.40)
>DroSec_CAF1 6327 99 - 1
UUUUAAUAAAAUUGGUUUUUCAAAUUUCAAUUCGCCGCAAUCGAUAGGAACUGUAGUUGCGGCGAAGAAAUGGAACUGGAACCGGAACCAGCAACGAAC
...........((((((((((...(((((.(((((((((((..((((...)))).)))))))))))....)))))...)))...)))))))........ ( -28.70)
>DroSim_CAF1 6221 99 - 1
UUUCAAUAAAAUUGGUUUUUCAAAUUUCAAUUCGCCGCAACCGAUAGGAACUGUAGUUGCGGCGAAGAAAUGGAACUGGAACCGGAACCAGCAACGAAC
...........((((((((((...(((((.(((((((((((..((((...)))).)))))))))))....)))))...)))...)))))))........ ( -30.20)
>DroEre_CAF1 6274 92 - 1
UUUCAGUAAAAUA-GUUAUUAAAACUCCAAUUCGCCGGAACCGAUAGACACUGUAGUUGCGGCGAAGA------UCGUGAGCCGGAACCGGCAUCGAAU
.............-................(((((((.(((..((((...)))).))).)))))))..------(((...((((....))))..))).. ( -26.10)
>DroYak_CAF1 6626 86 - 1
UUUCAAUAAAAUU-GUUUUUCAAAUUCCAAUUCGCCGCAACCGAUAGACACCGUAUUUGCGGCGAAGA------ACUUG------AACCGGCUCCGAAU
.............-....(((((.(((...((((((((((.((........))...))))))))))))------).)))------)).((....))... ( -21.60)
>consensus
UUUCAAUAAAAUUGGUUUUUCAAAUUCCAAUUCGCCGCAACCGAUAGGCACUGUAGUUGCGGCGAAGAAAUGGAACUUGAACCGGAACCAGCAACGAAC
...........(((((((............(((((((((((..((((...)))).)))))))))))............))))))).............. (-18.10 = -20.11 +   2.01)

alignment

secondary structure

dotplot

Window 0

Location	19,063,873 – 19,063,974
Length	101
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	78.91
Mean single sequence MFE	-23.90
Consensus MFE	-17.35
Energy contribution	-18.07
Covariance contribution	0.72
Combinations/Pair	1.09
Mean z-score	-2.75
Structure conservation index	0.73
SVM decision value	2.66
SVM RNA-class probability	0.996167
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19063873 101 + 20766785
UCUUCGCCGCAACUACAGUGCCUAUCGGUUGCGGCGAAUUGCAAUUUUAAAAACCAAUUUUGUUGAAAUUCGAAAGUAAAUGUAACGAAGACUUGCAAAUU--
..((((((((((((............))))))))))))((((((.((...........(((((((.....(....)......))))))))).))))))...-- ( -28.20)
>DroSec_CAF1 6358 103 + 1
UCUUCGCCGCAACUACAGUUCCUAUCGAUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUAAAAUUCAAAAGUAAAUAUAACGAAGACCUACAAAAUAG
((((((((((((................)))))))...(((((.(((((.(((.....))).))))).))))).............)))))............ ( -19.79)
>DroSim_CAF1 6252 103 + 1
UCUUCGCCGCAACUACAGUUCCUAUCGGUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUGAAAUUCAAAAGUAAACAUAACGAAGACCUACAAAAUAG
((((((((((((((............)))))))))(((((.(((.(((......))).))).....)))))...............)))))............ ( -24.40)
>DroEre_CAF1 6299 92 + 1
UCUUCGCCGCAACUACAGUGUCUAUCGGUUCCGGCGAAUUGGAGUUUUAAUAAC-UAUUUUACUGAAAUCCC------CUUCAUACGAAAUU----GGAAAUU
..(((((((.((((............)))).)))))))..((..(((((.(((.-....))).)))))..))------.((((........)----))).... ( -17.40)
>DroYak_CAF1 6645 102 + 1
UCUUCGCCGCAAAUACGGUGUCUAUCGGUUGCGGCGAAUUGGAAUUUGAAAAAC-AAUUUUAUUGAAAUUCCAAAGUACUUAUUACGAAGAUAUCCAGAAAAA
((((((((((((...((((....)))).)))))))...(((((((((.((.((.-....)).)).)))))))))............)))))............ ( -29.70)
>consensus
UCUUCGCCGCAACUACAGUGCCUAUCGGUUGCGGCGAAUUGAAAUUUGAAAAACCAAUUUUAUUGAAAUUCAAAAGUAAAUAUAACGAAGACCUACAAAAUAG
((((((((((((((............)))))))))(((((..(((................)))..)))))...............)))))............ (-17.35 = -18.07 +   0.72)

alignment

secondary structure

dotplot

Window 1

Location	19,063,873 – 19,063,974
Length	101
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	78.91
Mean single sequence MFE	-24.22
Consensus MFE	-17.06
Energy contribution	-17.50
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.01
Structure conservation index	0.70
SVM decision value	1.22
SVM RNA-class probability	0.932477
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19063873 101 - 20766785
--AAUUUGCAAGUCUUCGUUACAUUUACUUUCGAAUUUCAACAAAAUUGGUUUUUAAAAUUGCAAUUCGCCGCAACCGAUAGGCACUGUAGUUGCGGCGAAGA
--...((((((......((.......))(((..((..((((.....))))..))..)))))))))(((((((((((..((((...)))).))))))))))).. ( -26.50)
>DroSec_CAF1 6358 103 - 1
CUAUUUUGUAGGUCUUCGUUAUAUUUACUUUUGAAUUUUAAUAAAAUUGGUUUUUCAAAUUUCAAUUCGCCGCAAUCGAUAGGAACUGUAGUUGCGGCGAAGA
.......((((((.........)))))).((((((..(((((...)))))...))))))......(((((((((((..((((...)))).))))))))))).. ( -22.20)
>DroSim_CAF1 6252 103 - 1
CUAUUUUGUAGGUCUUCGUUAUGUUUACUUUUGAAUUUCAAUAAAAUUGGUUUUUCAAAUUUCAAUUCGCCGCAACCGAUAGGAACUGUAGUUGCGGCGAAGA
.......(((((.(........)))))).((((((..(((((...)))))...))))))......(((((((((((..((((...)))).))))))))))).. ( -25.90)
>DroEre_CAF1 6299 92 - 1
AAUUUCC----AAUUUCGUAUGAAG------GGGAUUUCAGUAAAAUA-GUUAUUAAAACUCCAAUUCGCCGGAACCGAUAGACACUGUAGUUGCGGCGAAGA
.......----.............(------(((.(((.(((((....-.))))).)))))))..(((((((.(((..((((...)))).))).))))))).. ( -22.10)
>DroYak_CAF1 6645 102 - 1
UUUUUCUGGAUAUCUUCGUAAUAAGUACUUUGGAAUUUCAAUAAAAUU-GUUUUUCAAAUUCCAAUUCGCCGCAACCGAUAGACACCGUAUUUGCGGCGAAGA
......((((.......(((.....)))(((((((...((((...)))-)..))))))).)))).((((((((((.((........))...)))))))))).. ( -24.40)
>consensus
CUAUUUUGUAGGUCUUCGUUAUAUUUACUUUGGAAUUUCAAUAAAAUUGGUUUUUCAAAUUCCAAUUCGCCGCAACCGAUAGGCACUGUAGUUGCGGCGAAGA
............(((((...............(((((..(((((((.....))))...)))..)))))((((((((..((((...)))).))))))))))))) (-17.06 = -17.50 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:37 2006