Locus 310

Sequence ID	3L_DroMel_CAF1
Location	905,651 – 905,788
Length	137
Max. P	0.965808

overview

Window 4

Location	905,651 – 905,759
Length	108
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	87.35
Mean single sequence MFE	-33.31
Consensus MFE	-25.85
Energy contribution	-26.85
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.78
SVM decision value	1.59
SVM RNA-class probability	0.965808
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 905651 108 + 23771897
UAUUGAACUGCCAGUUUGGCCUGACACACGCCAAACGCCAUGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC-------CAACUGGCCAACUGGGCAACU
........((((.(((((((.((...)).)))))))(((((.....(((((((....)))).....)))....)))))......(((-------.....)))......))))... ( -33.50)
>DroSec_CAF1 48169 105 + 1
UAUUGAACUGCCAGUUUGGCCUGACACACGACAAACGCCAUGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC-------CAACUGGCCAACUGGGCA---
..........((((((.((((.......((......(((((.....(((((((....)))).....)))....))))).....))..-------.....))))))))))...--- ( -30.14)
>DroEre_CAF1 51479 102 + 1
UAUUGAACUGCCAGUUUGGCCUGACACACGCCAAACGCCAUGAGAACGCUACCGCCUGGUCAAAAUGCGCAAACUGGCAAAAA--------CGCCAACUGGCCAACUGGC-----
.........(((((((.((((((((.((.((.....((.........))....)).))))))............((((.....--------.))))...)))))))))))----- ( -30.20)
>DroYak_CAF1 50424 115 + 1
UAUUGAACUGCCAGUUUGGCCUGACACACGCCAAACGCCAUGAGAACGCGACCAACUGGUCAAAAUGCACAAAAUGGCAAAAACGCCAACUGGCGAACUGGCGAACUGGCAAACU
........((((((((((......))..(((((..(((((.........((((....)))).............((((......))))..)))))...))))))))))))).... ( -39.40)
>consensus
UAUUGAACUGCCAGUUUGGCCUGACACACGCCAAACGCCAUGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC_______CAACUGGCCAACUGGCCA___
.........(((((((((((.((...)).)))))))(((((.....(((((((....)))).....)))....)))))....................))))............. (-25.85 = -26.85 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	905,651 – 905,759
Length	108
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	87.35
Mean single sequence MFE	-41.17
Consensus MFE	-31.06
Energy contribution	-32.38
Covariance contribution	1.31
Combinations/Pair	1.04
Mean z-score	-2.65
Structure conservation index	0.75
SVM decision value	1.46
SVM RNA-class probability	0.956283
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 905651 108 - 23771897
AGUUGCCCAGUUGGCCAGUUG-------GGCGUUUUUGCCAUUUUGCGCAUUUUGACCAGUCGGUCGCGUUCUCAUGGCGUUUGGCGUGUGUCAGGCCAAACUGGCAGUUCAAUA
..(((((.((((((((...((-------.(((((..((((((...((((.....((((....))))))))....))))))...))))).))...)))).)))))))))....... ( -41.20)
>DroSec_CAF1 48169 105 - 1
---UGCCCAGUUGGCCAGUUG-------GGCGUUUUUGCCAUUUUGCGCAUUUUGACCAGUCGGUCGCGUUCUCAUGGCGUUUGUCGUGUGUCAGGCCAAACUGGCAGUUCAAUA
---((((.((((((((...((-------.(((....((((((...((((.....((((....))))))))....)))))).....))).))...)))).))))))))........ ( -37.70)
>DroEre_CAF1 51479 102 - 1
-----GCCAGUUGGCCAGUUGGCG--------UUUUUGCCAGUUUGCGCAUUUUGACCAGGCGGUAGCGUUCUCAUGGCGUUUGGCGUGUGUCAGGCCAAACUGGCAGUUCAAUA
-----(((((((((((..((((((--------....))))))...........((((((.((.(.((((((.....))))))).)).)).)))))))).)))))))......... ( -42.50)
>DroYak_CAF1 50424 115 - 1
AGUUUGCCAGUUCGCCAGUUCGCCAGUUGGCGUUUUUGCCAUUUUGUGCAUUUUGACCAGUUGGUCGCGUUCUCAUGGCGUUUGGCGUGUGUCAGGCCAAACUGGCAGUUCAAUA
...((((((((((((((....(((((.(((((....)))))..))).)).....((((....)))).........)))))..((((.((...)).)))))))))))))....... ( -43.30)
>consensus
___UGCCCAGUUGGCCAGUUG_______GGCGUUUUUGCCAUUUUGCGCAUUUUGACCAGUCGGUCGCGUUCUCAUGGCGUUUGGCGUGUGUCAGGCCAAACUGGCAGUUCAAUA
.....(((((((((((.....................(((((...((((.....((((....))))))))....)))))...((((....)))))))).)))))))......... (-31.06 = -32.38 +   1.31)

alignment

secondary structure

dotplot

Window 6

Location	905,691 – 905,788
Length	97
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	76.16
Mean single sequence MFE	-27.47
Consensus MFE	-16.80
Energy contribution	-16.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.61
SVM decision value	0.12
SVM RNA-class probability	0.595490
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 905691 97 + 23771897
UGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC-------CAACUGGCCAACUGGGCAACUGGGCAACUGGGCAGCUGGCUAACC------CAAAC
.......((((((....))))....(((((......))......(((-------((..((.((....)).))..)))))......)))))(((.....)------))... ( -28.40)
>DroSec_CAF1 48209 95 + 1
UGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC-------CAACUGGCCAACUGGGCA--------ACUGGGCAGCUGGCUAACCUAAACCCAAAC
.......((((((....)))).....((((......))......(((-------((..((.((....)).))--------..))))).))..))................ ( -26.00)
>DroYak_CAF1 50464 105 + 1
UGAGAACGCGACCAACUGGUCAAAAUGCACAAAAUGGCAAAAACGCCAACUGGCGAACUGGCGAACUGGCAAACUGACGAACUGUGCAACUGGC-----GAAAUCGGAAC
.((...(((((((....))))....((((((............((((....)))).....((......))............))))))....))-----)...))..... ( -28.00)
>consensus
UGAGAACGCGACCGACUGGUCAAAAUGCGCAAAAUGGCAAAAACGCC_______CAACUGGCCAACUGGGCAACUG___AACUGGGCAGCUGGCUAACC_AAA_CCAAAC
.......((((((....))))....(((.((....(((......)))..........(..(....)..).............)).)))....))................ (-16.80 = -16.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:57 2006