Locus 4239

Sequence ID	2L_DroMel_CAF1
Location	12,116,964 – 12,117,156
Length	192
Max. P	0.543934

overview

Window 3

Location	12,116,964 – 12,117,084
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.17
Mean single sequence MFE	-29.07
Consensus MFE	-21.26
Energy contribution	-21.78
Covariance contribution	0.52
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.73
SVM decision value	0.02
SVM RNA-class probability	0.543934
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12116964 120 + 22407834
CGAGUUAAUGAGCUUACAAAGCCACUUGAUAUCUUUAAGGUAUCAAAAGAACUUCCUGACUGCCCUUUGGUCAUCUCGAUAAUCUGACCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
((((((..((.((.......(((((((((((((.....))))))))..................(((((((((...........))))))))).)))))..))))..))))))....... ( -32.00)
>DroSec_CAF1 19096 120 + 1
CGAGUUAAUAAGCUAACAAAGUCACUUGAUAUCUUUAAGCUAUCAAAAGAACUUCCUGACUGCCCUUUGGUCAUCUCGAUAAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
((((((.............((((..((((((.(.....).)))))).((......))))))...(((((((((...........)))))))))(((((....)))))))))))....... ( -27.30)
>DroSim_CAF1 18982 120 + 1
CGAGUUAAUGAGCUUACAAAGUCACUUGAUAUCUUUAAGGUAUCAAAAGAACUUCCUGACUGCCCUUUGGUCAUCUCGAUAAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
((((((..((.((.....(((((..((((((((.....))))))))..).))))....((..(.(((((((((...........))))))))).)..))..))))..))))))....... ( -32.30)
>DroEre_CAF1 19380 112 + 1
--------UGAUCUUACAAAGUUACUCGAUAUUGUAAAGGUAUCAAAUGAACUUCCUGAAUGCCCUUUGGUCAUCUCGAUAAUCUUGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
--------(((((((((((.(((....))).)))))).(((((((...........)).)))))....)))))....(((((((.........(((((....))))).....))))))). ( -24.14)
>DroYak_CAF1 19305 120 + 1
CGAGUUAAUGGGCUUACAACGUCACUCGAUAUCUUUAAGGUAUCAAAUGAACUUCCUGAAUGCCCUUCGGUCAUCUCGAUAAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
((((((...((((...((...(((...((((((.....))))))...)))......))...))))...(((((...........)))))....(((((....)))))))))))....... ( -29.60)
>consensus
CGAGUUAAUGAGCUUACAAAGUCACUUGAUAUCUUUAAGGUAUCAAAAGAACUUCCUGACUGCCCUUUGGUCAUCUCGAUAAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCA
...................((((....((((((.....))))))....(((.............(((((((((...........)))))))))(((((....)))))..))))))).... (-21.26 = -21.78 +   0.52)

alignment

secondary structure

dotplot

Window 4

Location	12,117,044 – 12,117,156
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.93
Mean single sequence MFE	-33.80
Consensus MFE	-28.66
Energy contribution	-29.14
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.23
Structure conservation index	0.85
SVM decision value	-0.04
SVM RNA-class probability	0.513276
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12117044 112 + 22407834
AAUCUGACCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUG---AGCUUCGACCGCCAUCUCAAGGUCGAAAAAAAAAGUAUCUUGUAUCU-GGUAUCUGGUAU----
......((((...(((((....))))).....(((.((((((..((((((((.---...(((((((..........)))))))......))).)))))..)))-))))))))))..---- ( -34.50)
>DroSec_CAF1 19176 114 + 1
AAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUGCUAAGCUUCGACCGCCAUCUCAAGGUCGAAAA--AAAGUAUCUUGUAUCUUGGUAUCCGGUAU----
..(((((((....(((((....))))).....(.....)..))))))).(((....)))(((((((..........)))))))..--...(((((..((((....))))..)))))---- ( -34.20)
>DroSim_CAF1 19062 114 + 1
AAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUGCUAAGCUUCGACCGCCAUCUCAAGGUCGAAAA--AAAGUAUCUUGUAUCUGGGUAUCUGGUAU----
..(((((((....(((((....))))).....(.....)..))))))).(((....)))(((((((..........)))))))..--...(((((..((((....))))..)))))---- ( -35.10)
>DroEre_CAF1 19452 113 + 1
AAUCUUGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUG---AGCUUCGACCGCCAUCUCAAGGUCGGAA---AAAGUAUCUUGUGUCUU-GUAUCUUGUAUCUGG
.......(((...(((((....))))).....(((...((((((((((((((.---...(((((((..........))))))).---..))).))))).)))))-).))).......))) ( -33.10)
>DroYak_CAF1 19385 109 + 1
AAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUG---AGCCUCGACCGCCAUCUCAAGGUCGAAA---AAAGUAUCUCGUAUCUU-GUAUCUGGUAU----
......((((...(((((....))))).....(((...(((((.((((((((.---....((((((..........))))))..---..))).)))))..))))-).)))))))..---- ( -32.10)
>consensus
AAUCUGGCCAAAGUGUGGUGUGCCACAAAUUCGAUUAUCAGGGCCGGGAGCUG___AGCUUCGACCGCCAUCUCAAGGUCGAAAA__AAAGUAUCUUGUAUCUUGGUAUCUGGUAU____
..(((((((....(((((....))))).....(.....)..))))))).(((....)))(((((((..........))))))).......(((((..((((....))))..))))).... (-28.66 = -29.14 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:11 2006