Locus 8545

Sequence ID	3R_DroMel_CAF1
Location	22,816,165 – 22,816,328
Length	163
Max. P	0.976823

overview

Window 2

Location	22,816,165 – 22,816,259
Length	94
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	96.02
Mean single sequence MFE	-27.50
Consensus MFE	-24.66
Energy contribution	-25.10
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.90
SVM decision value	1.78
SVM RNA-class probability	0.976823
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22816165 94 + 27905053
UCAAAUCGGAACUGGUCAAGUGCAAGUGGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCUGACCGGCA--
...........((((((...(((..((((.(((.....))).))))....)))...(((((((((.((......)).)))))))))))))))..-- ( -33.00)
>DroSec_CAF1 25096 96 + 1
UCAAAUCGGAACUGGUCAAGUGCAAGUCGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCUGGCCGGCAAA
.......((((((.(((..((((.....))))))).)))..)))....((((....(((((((((.((......)).))))))))).))))..... ( -28.30)
>DroSim_CAF1 25463 96 + 1
UCAAAUCGGAACUGGUCAAGUGCAAGUCGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCUGGCCGGCAAA
.......((((((.(((..((((.....))))))).)))..)))....((((....(((((((((.((......)).))))))))).))))..... ( -28.30)
>DroEre_CAF1 25110 94 + 1
UCAAAUCGGAACUGGUCAAGUGCAAGUCGCGCGAUAAGUGCUCCAUAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAACUGGCCGGCA--
...........(((((((.((....(..((((.....))))..)....((((((((((.((.......)).))))..)))))))))))))))..-- ( -23.80)
>DroYak_CAF1 25293 94 + 1
UCAAAUCGGAACUGGUCAAGUGCAAGUUGGGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAUCUGGCCGGCA--
...........(((((((.......((.(((((.....))))).)).(((((((((((.((.......)).))))..))))))).)))))))..-- ( -24.10)
>consensus
UCAAAUCGGAACUGGUCAAGUGCAAGUCGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCUGGCCGGCA__
...........((((((..((((.....))))......((((.......))))...(((((((((.((......)).))))))))))))))).... (-24.66 = -25.10 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	22,816,187 – 22,816,289
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.32
Mean single sequence MFE	-32.75
Consensus MFE	-18.99
Energy contribution	-18.97
Covariance contribution	-0.03
Combinations/Pair	1.24
Mean z-score	-2.08
Structure conservation index	0.58
SVM decision value	-0.04
SVM RNA-class probability	0.513433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22816187 102 + 27905053
-----CAAGUGGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCU-GACCGGCA--------AACAGAGAUGACGGCCCACUA----AAGAGCCGA
-----...((((.(((.....))).))))..((((....(((((((((.((......)).)))))))))-....(((.--------..((....))...))).....----....)))). ( -31.90)
>DroPse_CAF1 28705 107 + 1
-----GUGGCCUGGCGAUAAGUGCUCCACAAUGGCAGAGUGCGGGCAAAUAUAUUUUUAAUUGCCAGUUAGGCUGGCA--------AACAGAAAUGACGGCCCACAAGCGCAAGAGUCCG
-----(.(((((.(((....(..(((..(....)..)))..)((((.....(((((((..(((((((.....))))))--------)..)))))))...)))).....))).)).)))). ( -36.90)
>DroSim_CAF1 25485 110 + 1
-----CAAGUCGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCU-GGCCGGCAAACAGGCAAACAGAGAUGACGGCCCACUA----AAGAGCCGA
-----...(..((((.....))))..)....((((....(((((((((.((......)).)))))))))-(((((((......))...((....)).))))).....----....)))). ( -34.70)
>DroEre_CAF1 25132 102 + 1
-----CAAGUCGCGCGAUAAGUGCUCCAUAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAACU-GGCCGGCA--------AACAGAGAUGACGGCCCACUA----AAGAGCCGA
-----...(..((((.....))))..)....((((....((.((((((.((......)).)))))).))-(((((.((--------........)).))))).....----....)))). ( -27.00)
>DroYak_CAF1 25315 102 + 1
-----CAAGUUGGGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAUCU-GGCCGGCA--------AACAGAGAUGACGGCCCACUA----AAGACCCGA
-----....((((((....((((.......(((((((((((.((.......)).))))..)))))))..-(((((.((--------........)).))))))))).----..).))))) ( -26.80)
>DroPer_CAF1 28350 112 + 1
AGGGAAGGGCCUGGCAAUAAGUGCUCCACAAUGGCAGAGUGCGGGCAAAUAUAUUUUUAAUUGCCAGUUAGGCUGGCA--------AACAGAAAUGACGGCCCACAAGCGCAAGAGUCCG
......((((((.((.....(..(((..(....)..)))..)((((.....(((((((..(((((((.....))))))--------)..)))))))...))))......)).)).)))). ( -39.20)
>consensus
_____CAAGUCGCGCGAUAAGUGCUCCACAAUGGCAAAGAGCUGGUAAAUACAUUUUUAAUUGCCAGCU_GGCCGGCA________AACAGAGAUGACGGCCCACUA____AAGAGCCGA
.............(((.....)))........(((.....((((((((.((......)).))))))))..(((((......................))))).............))).. (-18.99 = -18.97 +  -0.03)

alignment

secondary structure

dotplot

Window 4

Location	22,816,222 – 22,816,328
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.71
Mean single sequence MFE	-27.17
Consensus MFE	-16.19
Energy contribution	-16.30
Covariance contribution	0.11
Combinations/Pair	1.22
Mean z-score	-1.84
Structure conservation index	0.60
SVM decision value	-0.01
SVM RNA-class probability	0.526164
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22816222 106 + 27905053
GCUGGUAAAUACAUUUUUAAUUGCCAGCU-GACCGGCA--------AACAGAGAUGACGGCCCACUA----AAGAGCCGAAAUGAAAAGGCAAA-UGGAAAGACCAACGCGGACGGACAA
((((((((.((......)).))))))))(-(.(((...--------...........((((.(....----..).))))..........((...-(((.....)))..))...))).)). ( -25.00)
>DroPse_CAF1 28740 112 + 1
GCGGGCAAAUAUAUUUUUAAUUGCCAGUUAGGCUGGCA--------AACAGAAAUGACGGCCCACAAGCGCAAGAGUCCGAAUGAAAAGGCAAAACCAAAAGACUACAGCGGCCUGACAA
...(((((.((......)).))))).(((((((.(((.--------..((....))...)))......(((...((((....(....)((.....))....))))...)))))))))).. ( -32.10)
>DroSim_CAF1 25520 101 + 1
GCUGGUAAAUACAUUUUUAAUUGCCAGCU-GGCCGGCAAACAGGCAAACAGAGAUGACGGCCCACUA----AAGAGCCGAAAUGAAAAGGCAAA-UGGAAAGACCAA-------------
((((((((.((......)).)))))))).-(((((((......))...((....)).))))).....----....(((..........)))...-(((.....))).------------- ( -27.40)
>DroEre_CAF1 25167 106 + 1
GCUGGUAAAUACAUUUUUAAUUGCCAACU-GGCCGGCA--------AACAGAGAUGACGGCCCACUA----AAGAGCCGAAAUGAAAAGGCAAA-UGGAAAGACCUACGCGGCCUGACAA
(((((((......((((((.(((((..((-(.......--------..)))......((((.(....----..).)))).........))))).-))))))....))).))))....... ( -25.10)
>DroYak_CAF1 25350 106 + 1
GCUGGUAAAUACAUUUUUAAUUGCCAUCU-GGCCGGCA--------AACAGAGAUGACGGCCCACUA----AAGACCCGAAAUGAAAAGGCAAA-UGGAAAGACCAAAGCGGCCUGACAA
((((.(.......((((((.(((((....-(((((.((--------........)).))))).....----...........(....)))))).-))))))......).))))....... ( -22.52)
>DroPer_CAF1 28390 112 + 1
GCGGGCAAAUAUAUUUUUAAUUGCCAGUUAGGCUGGCA--------AACAGAAAUGACGGCCCACAAGCGCAAGAGUCCGAAUGAAAAGGCAAAACGAAAAGACUACAGCGGCCUGACAA
...(((((.((......)).))))).(((((((.(((.--------..((....))...)))......(((...((((((..((......))...))....))))...)))))))))).. ( -30.90)
>consensus
GCUGGUAAAUACAUUUUUAAUUGCCAGCU_GGCCGGCA________AACAGAGAUGACGGCCCACUA____AAGAGCCGAAAUGAAAAGGCAAA_UGGAAAGACCAAAGCGGCCUGACAA
((((((((.((......)).))))))))..(((((......................))))).............(((..........)))............................. (-16.19 = -16.30 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:47 2006