Locus 7625

Sequence ID	3R_DroMel_CAF1
Location	20,434,234 – 20,434,368
Length	134
Max. P	0.952286

overview

Window 6

Location	20,434,234 – 20,434,347
Length	113
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	93.60
Mean single sequence MFE	-14.46
Consensus MFE	-12.44
Energy contribution	-12.64
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.86
SVM decision value	0.86
SVM RNA-class probability	0.869565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20434234 113 + 27905053
GCAAAAAAAAAAAAAGCGCAGCAUUUUAACAAGUUAAACAAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
................((((..((((.......(((.((.......(((.---.....)))....(((((.........))))))).))).......))))..))))......... ( -15.44)
>DroSec_CAF1 16838 105 + 1
GUAAAA-------AAGAGCAGCAUUUUAACAAGU-AAACAAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
......-------.....................-...............---..((((((....(((((.........)))))((((..............)))))))))).... ( -13.04)
>DroSim_CAF1 16499 105 + 1
GCAAAA-------AAGAGCAGCAUUUUAACAAGU-AAACAAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
((....-------....))...............-...............---..((((((....(((((.........)))))((((..............)))))))))).... ( -14.04)
>DroEre_CAF1 16450 105 + 1
GCAAAA-------AAGAGCAACGUUUUAACAAGU-AAACAAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
((....-------....))...((((........-))))...........---..((((((....(((((.........)))))((((..............)))))))))).... ( -15.24)
>DroYak_CAF1 17474 108 + 1
GCAAAA-------AAGAGCAACAUUUUAACAAGU-AAACAAUCAAAGAUAUCAUCGUACUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
((....-------....))..(((((((((....-...........(((...)))((((....))))......))))))))).(((((..............)))))......... ( -14.54)
>consensus
GCAAAA_______AAGAGCAGCAUUUUAACAAGU_AAACAAUCAAAGAAA___UCGUAUUCAAGUGCCACAAAGUUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAU
.......................................................((((((....(((((.........)))))((((..............)))))))))).... (-12.44 = -12.64 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	20,434,273 – 20,434,368
Length	95
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	75.53
Mean single sequence MFE	-17.71
Consensus MFE	-10.83
Energy contribution	-10.97
Covariance contribution	0.14
Combinations/Pair	1.25
Mean z-score	-1.97
Structure conservation index	0.61
SVM decision value	1.42
SVM RNA-class probability	0.952286
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20434273 95 + 27905053
AAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAG-UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUCAAGAUACGCA-------------------ACUUGAAAAG
...........---.....((((((((((((....-.....)))))...................((((.((..........)).))))-------------------)))))))... ( -17.50)
>DroSec_CAF1 16869 95 + 1
AAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAG-UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUAAAGAUAUGCU-------------------ACUUGAAAAG
...........---.....((((((((((((....-.....)))))((((..............)))).....................-------------------)))))))... ( -15.04)
>DroSim_CAF1 16530 95 + 1
AAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAG-UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUAAAGAUAUGCA-------------------ACUUGAAAAG
...........---.....((((((((((((....-.....)))))...................(((..((((........)))))))-------------------)))))))... ( -16.20)
>DroEre_CAF1 16481 108 + 1
AAUCAAAGAAA---UCGUAUUCAAGUGCCACAAAG-UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUAUAGAUAUGCA------ACUCACAGCGACGACUUGAAAAG
...........---.....((((((((((((....-.....)))))...................((((..(((....)))....))))------.............)))))))... ( -16.50)
>DroYak_CAF1 17505 114 + 1
AAUCAAAGAUAUCAUCGUACUCAAGUGCCACAAAG-UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUAUAGAUAUGCA--G-CGAUUCACAGCGACGUCUUGAAAAG
..((((.((..((.(((((.......(((((....-.....)))))((.........))......)))))...................--(-(........))))..)))))).... ( -19.00)
>DroAna_CAF1 17444 112 + 1
AGUAAUACAGA---UCUUUUUCAAGUGCUGCCUACAUU---GUGUUGAAAGAAGCGAAAAAAUAUUACGAAAAUAAAGUGAGAUAUCAGAAGUCGGCAUGCAUGAAAGAGUUGAAAUG
.......(((.---.((((((((..(((((((.((.((---((.((....)).)))).......((((.........))))..........)).)))).))))))))))))))..... ( -22.00)
>consensus
AAUCAAAGAAA___UCGUAUUCAAGUGCCACAAAG_UUGAAGUGGCGUAUAAAAUAAACAAAUAAUGCGAAUAUAAAUAAAGAUAUGCA___________________ACUUGAAAAG
...................((((((((((((..........)))))((((..............))))........................................)))))))... (-10.83 = -10.97 +   0.14)

alignment

secondary structure

dotplot

Window 8

Location	20,434,273 – 20,434,368
Length	95
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	75.53
Mean single sequence MFE	-16.94
Consensus MFE	-8.97
Energy contribution	-10.00
Covariance contribution	1.03
Combinations/Pair	1.07
Mean z-score	-1.75
Structure conservation index	0.53
SVM decision value	0.36
SVM RNA-class probability	0.705769
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20434273 95 - 27905053
CUUUUCAAGU-------------------UGCGUAUCUUGAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA-CUUUGUGGCACUUGAAUACGA---UUUCUUUGAUU
...(((((((-------------------((((................))))...................(((((.....-....)))))))))))).....---........... ( -17.49)
>DroSec_CAF1 16869 95 - 1
CUUUUCAAGU-------------------AGCAUAUCUUUAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA-CUUUGUGGCACUUGAAUACGA---UUUCUUUGAUU
...(((((((-------------------.....................(((.....)))...........(((((.....-....)))))))))))).....---........... ( -15.40)
>DroSim_CAF1 16530 95 - 1
CUUUUCAAGU-------------------UGCAUAUCUUUAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA-CUUUGUGGCACUUGAAUACGA---UUUCUUUGAUU
...(((((((-------------------(((((((........))))..)))...................(((((.....-....)))))))))))).....---........... ( -15.20)
>DroEre_CAF1 16481 108 - 1
CUUUUCAAGUCGUCGCUGUGAGU------UGCAUAUCUAUAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA-CUUUGUGGCACUUGAAUACGA---UUUCUUUGAUU
...(((((((.(((((...((((------((......((((...(((...(((.....))).)))..))))........)))-))).)))))))))))).....---........... ( -19.64)
>DroYak_CAF1 17505 114 - 1
CUUUUCAAGACGUCGCUGUGAAUCG-C--UGCAUAUCUAUAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA-CUUUGUGGCACUUGAGUACGAUGAUAUCUUUGAUU
....((((((..((((.(((...))-)--.))..........(..((((((((.....)))...........(((((.....-....)))))....)))))..).))..)).)))).. ( -21.00)
>DroAna_CAF1 17444 112 - 1
CAUUUCAACUCUUUCAUGCAUGCCGACUUCUGAUAUCUCACUUUAUUUUCGUAAUAUUUUUUCGCUUCUUUCAACAC---AAUGUAGGCAGCACUUGAAAAAGA---UCUGUAUUACU
........((.((((((((.((((.((...(((....)))...((((.....)))).....................---...)).)))))))..))))).)).---........... ( -12.90)
>consensus
CUUUUCAAGU___________________UGCAUAUCUUUAUUUAUAUUCGCAUUAUUUGUUUAUUUUAUACGCCACUUCAA_CUUUGUGGCACUUGAAUACGA___UUUCUUUGAUU
...(((((((........................................(((.....)))...........(((((..........))))))))))))................... ( -8.97 = -10.00 +   1.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:32 2006