Locus 5075

Sequence ID	2L_DroMel_CAF1
Location	14,506,126 – 14,506,265
Length	139
Max. P	0.904488

overview

Window 7

Location	14,506,126 – 14,506,225
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-20.59
Consensus MFE	-15.68
Energy contribution	-16.44
Covariance contribution	0.76
Combinations/Pair	1.10
Mean z-score	-1.76
Structure conservation index	0.76
SVM decision value	0.15
SVM RNA-class probability	0.606766
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14506126 99 + 22407834
GACAUAUGACUGUCAGACUUUUCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAA
((((((.((.(((((((((..(((((...........)))))..))....))))))).)).)))))).......((((((((....)))).)))).... ( -22.60)
>DroSec_CAF1 37783 99 + 1
GACAUAUGACUGUCAGACUUUUCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAA
((((((.((.(((((((((..(((((...........)))))..))....))))))).)).)))))).......((((((((....)))).)))).... ( -22.60)
>DroSim_CAF1 22486 99 + 1
GACAUAUGACUGUCAGACUUCUCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAA
((((((.((.(((((((((..(((((...........)))))..))....))))))).)).)))))).......((((((((....)))).)))).... ( -21.80)
>DroEre_CAF1 31343 98 + 1
GACGUAUGACUGGCAGCCUCUUCCUU-UUUCAUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGUAUUCAAAUUCUGCGACUAA
.(((((.....(((....((((....-...........))))...)))((((((((((....))))))))))...)))))................... ( -17.76)
>DroYak_CAF1 27047 98 + 1
GGCAUAUGACUGUCAGCCGUUUCUUU-UUUCUUGUCCAAAGAUUAGCCACUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAACUCUGCGACUAG
((((((.((.((((((..((..((..-..((((.....))))..))..)).)))))).)).))))))..........((((.........))))..... ( -18.20)
>consensus
GACAUAUGACUGUCAGACUUUUCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAA
((((......))))...............((((.....))))((((..((((((((((....))))))))))..((((((((....)))).)))))))) (-15.68 = -16.44 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	14,506,126 – 14,506,225
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-21.40
Consensus MFE	-17.02
Energy contribution	-17.14
Covariance contribution	0.12
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.80
SVM decision value	1.04
SVM RNA-class probability	0.904488
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14506126 99 - 22407834
UUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGAAAAGUCUGACAGUCAUAUGUC
((((((((.((((....))))))....(((((((((......)))))))))))))))(((((...........))))).......((((......)))) ( -22.60)
>DroSec_CAF1 37783 99 - 1
UUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGAAAAGUCUGACAGUCAUAUGUC
((((((((.((((....))))))....(((((((((......)))))))))))))))(((((...........))))).......((((......)))) ( -22.60)
>DroSim_CAF1 22486 99 - 1
UUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGAGAAGUCUGACAGUCAUAUGUC
...(((((.((((....))))))....(((((((((......)))))))))((((..(((((...........)))))..)))).)))........... ( -23.10)
>DroEre_CAF1 31343 98 - 1
UUAGUCGCAGAAUUUGAAUACGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAUGAAA-AAGGAAGAGGCUGCCAGUCAUACGUC
((((((.....(((((......)))))(((((((((......)))))))))))))))(((((..........-)))))...(((.....)))....... ( -18.10)
>DroYak_CAF1 27047 98 - 1
CUAGUCGCAGAGUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAGUGGCUAAUCUUUGGACAAGAAA-AAAGAAACGGCUGACAGUCAUAUGCC
.(((((((...(((((......)))))..(((((((......)))))))))))))).(((((..........-)))))...(((............))) ( -20.60)
>consensus
UUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGAAAAGUCUGACAGUCAUAUGUC
((((((((.((((....))))))....(((((((((......)))))))))))))))(((((...........)))))..................... (-17.02 = -17.14 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	14,506,147 – 14,506,265
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	92.40
Mean single sequence MFE	-26.30
Consensus MFE	-21.00
Energy contribution	-22.20
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.80
SVM decision value	0.21
SVM RNA-class probability	0.634793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14506147 118 + 22407834
UCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAAAAAAAAAAUGAACUUUAAGGCGACUUGAGCGAUAGGUAAA
.........(((((((.(((....(((((((((((((....))))))))))..((((((((....)))).))))......................)))..)))..).)))))).... ( -26.90)
>DroSec_CAF1 37804 116 + 1
UCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAAAA--AAAAUGAACUGGAAGGCGACUUGAGCGAUAGGUAAA
.........(((((((.(((....(((((((((((((....))))))))))..((((((((....)))).))))......--..............)))..)))..).)))))).... ( -26.90)
>DroSim_CAF1 22507 115 + 1
UCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAAA---AAAAUGAACUGGAAGGCGACUUGAGCGAUAGGUAAA
.........(((((((.(((....(((((((((((((....))))))))))..((((((((....)))).)))).....---..............)))..)))..).)))))).... ( -26.90)
>DroEre_CAF1 31364 116 + 1
UCCUU-UUUCAUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGUAUUCAAAUUCUGCGACUAAAC-AAAAAUGAGCUACAAGGCGACUUGAGCGAUAGGUAAA
.(((.-..((..(((...(((......((((((((((....))))))))))(((((......))))))))..))).....-........(((.((((....))))))))).))).... ( -26.30)
>DroYak_CAF1 27068 114 + 1
UCUUU-UUUCUUGUCCAAAGAUUAGCCACUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAACUCUGCGACUAG---GAAAAUGGGCUAGAAGCCGACUUGAGCGAUAGGUAAA
.....-...((((((......((((((..((((((((....)))))))).......((((.........)))).....---.......))))))..((........)))))))).... ( -24.50)
>consensus
UCUUUUUUUCUUGUCCAAAGAUUAGCCAUUUUGACAUUUUUGUGUCAAAAUAUUUGCGCAUUCAAAUGCUGCGACUAAA___AAAAUGAACUAGAAGGCGACUUGAGCGAUAGGUAAA
.........(((((((.(((....(((((((((((((....))))))))))..((((((((....)))).))))......................)))..)))..).)))))).... (-21.00 = -22.20 +   1.20)

alignment

secondary structure

dotplot

Window 0

Location	14,506,147 – 14,506,265
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	92.40
Mean single sequence MFE	-24.60
Consensus MFE	-18.64
Energy contribution	-19.16
Covariance contribution	0.52
Combinations/Pair	1.12
Mean z-score	-1.63
Structure conservation index	0.76
SVM decision value	0.01
SVM RNA-class probability	0.539489
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14506147 118 - 22407834
UUUACCUAUCGCUCAAGUCGCCUUAAAGUUCAUUUUUUUUUUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGA
................................((((((((((.(((((.((((....))))))...((((((((((......))))))))))...........))).)))))))))). ( -23.30)
>DroSec_CAF1 37804 116 - 1
UUUACCUAUCGCUCAAGUCGCCUUCCAGUUCAUUUU--UUUUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGA
......................(((..(((((....--..((((((((.((((....))))))....(((((((((......)))))))))))))))....)))))..)))....... ( -24.50)
>DroSim_CAF1 22507 115 - 1
UUUACCUAUCGCUCAAGUCGCCUUCCAGUUCAUUUU---UUUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGA
......................(((..(((((....---.((((((((.((((....))))))....(((((((((......)))))))))))))))....)))))..)))....... ( -25.10)
>DroEre_CAF1 31364 116 - 1
UUUACCUAUCGCUCAAGUCGCCUUGUAGCUCAUUUUU-GUUUAGUCGCAGAAUUUGAAUACGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAUGAAA-AAGGA
....(((...(((((((....)))).)))((((.(..-(.((((((.....(((((......)))))(((((((((......)))))))))))))))....)..).))))..-.))). ( -26.10)
>DroYak_CAF1 27068 114 - 1
UUUACCUAUCGCUCAAGUCGGCUUCUAGCCCAUUUUC---CUAGUCGCAGAGUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAGUGGCUAAUCUUUGGACAAGAAA-AAAGA
................((((((.....))).......---.(((((((...(((((......)))))..(((((((......)))))))))))))).......)))......-..... ( -24.00)
>consensus
UUUACCUAUCGCUCAAGUCGCCUUCCAGUUCAUUUU___UUUAGUCGCAGCAUUUGAAUGCGCAAAUAUUUUGACACAAAAAUGUCAAAAUGGCUAAUCUUUGGACAAGAAAAAAAGA
...........................(((((........((((((((.((((....))))))....(((((((((......)))))))))))))))....)))))............ (-18.64 = -19.16 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:21 2006