Locus 592

Sequence ID	3R_DroMel_CAF1
Location	2,198,871 – 2,198,984
Length	113
Max. P	0.852322

overview

Window 3

Location	2,198,871 – 2,198,963
Length	92
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.30
Mean single sequence MFE	-38.48
Consensus MFE	-25.83
Energy contribution	-26.50
Covariance contribution	0.67
Combinations/Pair	1.20
Mean z-score	-2.18
Structure conservation index	0.67
SVM decision value	0.73
SVM RNA-class probability	0.835017
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2198871 92 + 27905053
----GGU-----------CUUCUGGACGGUGCUGUAGCUGCUAGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA-
----(((-----------((((.(((.((((((((.((.....))..)))))))).)))(((.....)))...))))))).(..(((((((.....)))))))..).- ( -40.10)
>DroSec_CAF1 1904 92 + 1
----GGU-----------CUUCUGGACGGUGCUGUAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGUUGGGCCAAGGAGUUCUUGGUCUGCA-
----(((-----------((((.(((.((((((((.((.....))..)))))))).)))(((.....)))...)))))))...((((((((.....))))))))...- ( -37.20)
>DroSim_CAF1 1902 92 + 1
----GGU-----------CUUCUGGACGGUGCUGUAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUUCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA-
----(((-----------((((.(((.((((((((.((.....))..)))))))).)))(((.....)))...))))))).(..(((((((.....)))))))..).- ( -40.00)
>DroEre_CAF1 2230 92 + 1
----GGU-----------CUUCUGGGCGGUGCUGUAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCAAAGGAGUUCUUCGUCUGAA-
----(((-----------(.((.(((.((((((((.((.....))..)))))))).))).)).)))).((..((((((((.((......)).)).))))))..))..- ( -32.60)
>DroYak_CAF1 1906 92 + 1
----GGU-----------CUUCUGGGCGGUGCUGUAGCUGCUGGCGGGCAGCACAUUCUUGGCGAUACCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA-
----(((-----------((.(..((.((((.(((.((((((....)))))).((....))))).)))).))..)))))).(..(((((((.....)))))))..).- ( -37.80)
>DroPer_CAF1 15599 102 + 1
UGAUGAUGGUGCGGGGGGUUCCUUCCUGCUGCUGUAGCU---GGCGGGAUGCAG---CUUGGCAAGCGCAUUGGGCGACUGAUGUGUGAUGGAGCUCUUUGUCUGUAA
.....((((.((((((((((((.(((((((((....)).---)))))))(((..---....))).((((((..(....)..))))))...)))))))))))))))).. ( -43.20)
>consensus
____GGU___________CUUCUGGACGGUGCUGUAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA_
.......................((((.(((((((.((.....))..))))))).((((((((....(((...(....)...))))))))))).......)))).... (-25.83 = -26.50 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	2,198,890 – 2,198,984
Length	94
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	77.65
Mean single sequence MFE	-32.50
Consensus MFE	-13.95
Energy contribution	-13.98
Covariance contribution	0.03
Combinations/Pair	1.30
Mean z-score	-2.48
Structure conservation index	0.43
SVM decision value	0.79
SVM RNA-class probability	0.852322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2198890 94 + 27905053
UAGCUGCUAGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA----AAUCG-AAUGGGAUACAGAUUA
..((((((....))))))......(((...(((((((((((......(..(((((((.....)))))))..).----..)))-)))))))).))).... ( -39.00)
>DroPse_CAF1 12235 92 + 1
UAGCU---GGCGGGAUGCAG---CUUGGCAAGCGCAUUGGGCGACUGAUGUGUGAUGGAGCUCUUUGUCUGUAAGA-AAUUGCAUUGAGAUGAUAGUUA
(((((---(.(..(((((((---(((.(...((((((..(....)..))))))..).))))((((.......))))-...))))))..)....)))))) ( -28.80)
>DroSec_CAF1 1923 94 + 1
UAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGUUGGGCCAAGGAGUUCUUGGUCUGCA----AAUCG-AAUGGGAUAUGGAUUA
..((((((....))))))....(((.....(((((((((((....(((.((((((((.....)))))))))))----..)))-))))))))..)))... ( -35.80)
>DroSim_CAF1 1921 94 + 1
UAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUUCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA----AAUCA-AAUGGGAUAUUGAUUA
..((((((....))))))............(((((((((((......(..(((((((.....)))))))..).----..)))-))))))))........ ( -34.80)
>DroEre_CAF1 2249 94 + 1
UAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCAAAGGAGUUCUUCGUCUGAA----AUUCG-AAUAAGAUAUGGAUUA
..((((((....)))))).((((((..(((.((((....)).)).)))..)).)))).(((((...((((...----.....-....))))..))))). ( -27.80)
>DroPer_CAF1 15633 93 + 1
UAGCU---GGCGGGAUGCAG---CUUGGCAAGCGCAUUGGGCGACUGAUGUGUGAUGGAGCUCUUUGUCUGUAAGAAAAUUGCAUUGAGAUGAUAGUUA
(((((---(.(..(((((((---(((.(...((((((..(....)..))))))..).))))((((.......))))....))))))..)....)))))) ( -28.80)
>consensus
UAGCUGCUGGCGGGCAGCACUUUCUUGGCGAUCCCAUUUGGAGACUGCUGGGCCAAGGAGUUCUUGGUCUGGA____AAUCG_AAUGAGAUAUUGAUUA
..(((((......)))))....(((((.(((.((((...(....)...))))(((((.....)))))............)))...)))))......... (-13.95 = -13.98 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:56 2006