Locus 643

Sequence ID	3R_DroMel_CAF1
Location	2,381,328 – 2,381,436
Length	108
Max. P	0.779810

overview

Window 7

Location	2,381,328 – 2,381,436
Length	108
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	84.50
Mean single sequence MFE	-30.78
Consensus MFE	-21.21
Energy contribution	-21.30
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.69
SVM decision value	0.13
SVM RNA-class probability	0.596669
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2381328 108 + 27905053
UAGCUUUUUUGGCAAGCAUCCUGCUGAAUG----GAGGAA----GUGGUGCCACUUU-UUAUGCAUUCGACUGUGCAUAAGUAUGUAUAUACUUCUAUAUAUUUUUGGCCGGCCAAA
.......((((((..((.(((........)----))((((----(((((((.....(-((((((((......)))))))))...)))).)))))))...........))..)))))) ( -31.10)
>DroSec_CAF1 93942 108 + 1
UAGCUUUUUUGGCAAGCAUCCUGGUGAAUA----GAGGAA----CUGGUGCCACUUU-UUAUGCAUUCGACUGUGCAUAAGUAUGUAUAUACUUCUAUAUAUUUUUCGCCGGCCAAA
.......((((((..((.....((((.(((----((((..----...((((.....(-((((((((......)))))))))...))))...))))))).))))....))..)))))) ( -28.40)
>DroSim_CAF1 86632 108 + 1
UAGCUUUUUUGGCAAGCAUCCUGGUGAAUG----GAGGAA----CUGGUGCCACUUU-UUAUGCAUUCGACUGUGCAUAAGUAUGUAUAUACUUCUAUAUAUUUUUCGCCGGCCAAA
.......((((((..((.....((((.(((----((((..----...((((.....(-((((((((......)))))))))...))))...))))))).))))....))..)))))) ( -28.10)
>DroEre_CAF1 88148 103 + 1
-----UUUUUGGCAAGCAUCCUGCUGAAUG----GAGGAG----CUGGUGCCACUUU-UUAUGCAUUCGACUGUGCAUAAGUACGUAUAUACUUCUAUAUAUUUUUGGCCGGCCAAA
-----..((((((.(((.((((.(.....)----.)))))----)).(.((((...(-((((((((......)))))))))...(((((((....)))))))...))))).)))))) ( -33.10)
>DroYak_CAF1 82347 108 + 1
UAGCUUUUUUGGCAAGCAUCCUGCUGAAUG----GAGGAA----CUGGUGCCACUUU-UUAUGCAUUCGACUGUGCAUAAGUACGUAUAUAUUUCUAUAUAUUUUUGGCCGGCCAAA
.......((((((.....((((.(.....)----.)))).----...(.((((...(-((((((((......)))))))))...(((((((....)))))))...))))).)))))) ( -29.50)
>DroAna_CAF1 86569 106 + 1
UUUUAUUUUUGGCAAGCAUCCUUCUGAACAGCCAGAGGAGCUAGCUAGUGCUACUCUCCUAUGCAUCAGAGUGUGCAUAAAUACAUAUAUAUUUG-----------UGCCGGCCAAA
.......((((((..((((...(((((...((...(((((.((((....))))..)))))..)).)))))))))(((((((((......))))))-----------)))..)))))) ( -34.50)
>consensus
UAGCUUUUUUGGCAAGCAUCCUGCUGAAUG____GAGGAA____CUGGUGCCACUUU_UUAUGCAUUCGACUGUGCAUAAGUACGUAUAUACUUCUAUAUAUUUUUGGCCGGCCAAA
.......((((((..((.((((.............))))........((((.......((((((((......)))))))))))).......................))..)))))) (-21.21 = -21.30 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	2,381,328 – 2,381,436
Length	108
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	84.50
Mean single sequence MFE	-26.57
Consensus MFE	-20.85
Energy contribution	-20.44
Covariance contribution	-0.42
Combinations/Pair	1.13
Mean z-score	-2.30
Structure conservation index	0.78
SVM decision value	0.55
SVM RNA-class probability	0.779810
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2381328 108 - 27905053
UUUGGCCGGCCAAAAAUAUAUAGAAGUAUAUACAUACUUAUGCACAGUCGAAUGCAUAA-AAAGUGGCACCAC----UUCCUC----CAUUCAGCAGGAUGCUUGCCAAAAAAGCUA
((((((.(((...............(((((........)))))...((.(((((.....-.(((((....)))----))....----))))).)).....))).))))))....... ( -25.00)
>DroSec_CAF1 93942 108 - 1
UUUGGCCGGCGAAAAAUAUAUAGAAGUAUAUACAUACUUAUGCACAGUCGAAUGCAUAA-AAAGUGGCACCAG----UUCCUC----UAUUCACCAGGAUGCUUGCCAAAAAAGCUA
((((((.((((....((((((....)))))).(((..(((((((........)))))))-...))).......----.((((.----........)))))))).))))))....... ( -22.70)
>DroSim_CAF1 86632 108 - 1
UUUGGCCGGCGAAAAAUAUAUAGAAGUAUAUACAUACUUAUGCACAGUCGAAUGCAUAA-AAAGUGGCACCAG----UUCCUC----CAUUCACCAGGAUGCUUGCCAAAAAAGCUA
((((((.((((((..((((((....)))))).(((..(((((((........)))))))-...))).......----))).((----(........))).))).))))))....... ( -23.10)
>DroEre_CAF1 88148 103 - 1
UUUGGCCGGCCAAAAAUAUAUAGAAGUAUAUACGUACUUAUGCACAGUCGAAUGCAUAA-AAAGUGGCACCAG----CUCCUC----CAUUCAGCAGGAUGCUUGCCAAAAA-----
((((((..((((...((((((....))))))......(((((((........)))))))-....))))...((----(((((.----(.....).)))).))).))))))..----- ( -27.20)
>DroYak_CAF1 82347 108 - 1
UUUGGCCGGCCAAAAAUAUAUAGAAAUAUAUACGUACUUAUGCACAGUCGAAUGCAUAA-AAAGUGGCACCAG----UUCCUC----CAUUCAGCAGGAUGCUUGCCAAAAAAGCUA
((((((..((((....((((((....)))))).....(((((((........)))))))-....))))...((----(((((.----(.....).)))).))).))))))....... ( -27.10)
>DroAna_CAF1 86569 106 - 1
UUUGGCCGGCA-----------CAAAUAUAUAUGUAUUUAUGCACACUCUGAUGCAUAGGAGAGUAGCACUAGCUAGCUCCUCUGGCUGUUCAGAAGGAUGCUUGCCAAAAAUAAAA
((((((.((((-----------.((((((....)))))).....(..(((((.((..(((((..((((....)))).)))))...))...)))))..).)))).))))))....... ( -34.30)
>consensus
UUUGGCCGGCCAAAAAUAUAUAGAAGUAUAUACAUACUUAUGCACAGUCGAAUGCAUAA_AAAGUGGCACCAG____UUCCUC____CAUUCAGCAGGAUGCUUGCCAAAAAAGCUA
((((((.(((....................(((....(((((((........)))))))....)))............((((.............)))).))).))))))....... (-20.85 = -20.44 +  -0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:10 2006