Locus 8077

Sequence ID	3L_DroMel_CAF1
Location	21,269,145 – 21,269,345
Length	200
Max. P	0.939537

overview

Window 6

Location	21,269,145 – 21,269,265
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.14
Mean single sequence MFE	-34.67
Consensus MFE	-30.00
Energy contribution	-29.62
Covariance contribution	-0.38
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.87
SVM decision value	0.02
SVM RNA-class probability	0.541780
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269145 120 + 23771897
GUUAAUUACCUGGUAACUAUGGCUGAUCAUGCUUUUCAUCGGCCCGGGCCGCUGAAACAAGCGAACAAGGCUCACAAAACGGGUCGUCAUCGCUCCAAAGGAGCAAUAGACAAUGCCCAA
....................(((((((.(......).))))))).((((((((......)))).....(((((.......)))))(((((.(((((...))))).)).)))...)))).. ( -37.10)
>DroSec_CAF1 27422 120 + 1
GUUAAUUACCUGGUAACUAUGGCGGAUCAUGCAUUUCAUCGGCCCGGGCCGCUGAAACAAACGAACAAGGCUCACAAAACAGGUCGUCAUCGCUCCAAAGGAGCAAUAGACAAUGCCCAA
.......(((((........(((.(((.(......).))).))).(((((..((...........)).)))))......))))).(((((.(((((...))))).)).)))......... ( -31.00)
>DroSim_CAF1 29678 120 + 1
GUUAAUUACCUGCUAACUAUGGCGGAUCAUGCAUUUCAUCGGCCCGGGCCGCUGAAACAAACGAACAAGGCUCACAAAACAGGUCGUCAUCGCUCCAAAGGGGCAAUAGACAAUGCCCAA
.........((((((....)))))).....((((((((.((((....)))).)))))...........((((.........))))(((((.(((((...))))).)).)))..))).... ( -31.00)
>DroEre_CAF1 28598 119 + 1
GUUAAAUACCUG-UGACAAUGGCGGAUCAUGCGUUUCAUCGGCCCGGGCCGCUGAAGCAAACGAACAAGGCUCACAAAACGGGUCGUCAUCGCUCCAAAGGAGCAAUAGACAAUGCCCAA
..........((-((((..(((((.....)))((((((.((((....)))).)))))).......))..).)))))....((((.(((((.(((((...))))).)).)))...)))).. ( -39.60)
>consensus
GUUAAUUACCUGGUAACUAUGGCGGAUCAUGCAUUUCAUCGGCCCGGGCCGCUGAAACAAACGAACAAGGCUCACAAAACAGGUCGUCAUCGCUCCAAAGGAGCAAUAGACAAUGCCCAA
....................(((.((((.....(((((.((((....)))).))))).....((.......))........))))(((((.(((((...))))).)).)))...)))... (-30.00 = -29.62 +  -0.38)

alignment

secondary structure

dotplot

Window 7

Location	21,269,145 – 21,269,265
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.14
Mean single sequence MFE	-41.12
Consensus MFE	-36.67
Energy contribution	-37.55
Covariance contribution	0.88
Combinations/Pair	1.05
Mean z-score	-1.76
Structure conservation index	0.89
SVM decision value	0.52
SVM RNA-class probability	0.768869
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269145 120 - 23771897
UUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCCGUUUUGUGAGCCUUGUUCGCUUGUUUCAGCGGCCCGGGCCGAUGAAAAGCAUGAUCAGCCAUAGUUACCAGGUAAUUAAC
...(((.(((((.((((((((...)))))))))))))...(((((((((((...)))))).....(((.((((....)))).)))))))).......))).(((((((...))))))).. ( -41.50)
>DroSec_CAF1 27422 120 - 1
UUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCUGUUUUGUGAGCCUUGUUCGUUUGUUUCAGCGGCCCGGGCCGAUGAAAUGCAUGAUCCGCCAUAGUUACCAGGUAAUUAAC
........((((.((((((((...))))))))))))(((((..(((((.((.....((((.(((((((.((((....)))).))))))).))))...)))))))....)))))....... ( -42.30)
>DroSim_CAF1 29678 120 - 1
UUGGGCAUUGUCUAUUGCCCCUUUGGAGCGAUGACGACCUGUUUUGUGAGCCUUGUUCGUUUGUUUCAGCGGCCCGGGCCGAUGAAAUGCAUGAUCCGCCAUAGUUAGCAGGUAAUUAAC
........((((.(((((((....)).)))))))))((((((((((((.((.....((((.(((((((.((((....)))).))))))).))))...)))))))..)))))))....... ( -40.50)
>DroEre_CAF1 28598 119 - 1
UUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCCGUUUUGUGAGCCUUGUUCGUUUGCUUCAGCGGCCCGGGCCGAUGAAACGCAUGAUCCGCCAUUGUCA-CAGGUAUUUAAC
..(((..(((((.((((((((...))))))))))))))))..(((((((((.....((((.((.((((.((((....)))).)))).)).))))...)).....)))-))))........ ( -40.20)
>consensus
UUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCCGUUUUGUGAGCCUUGUUCGUUUGUUUCAGCGGCCCGGGCCGAUGAAAUGCAUGAUCCGCCAUAGUUACCAGGUAAUUAAC
..(((..(((((.((((((((...))))))))))))))))...(((((.((.....((((.(((((((.((((....)))).))))))).))))...)))))))................ (-36.67 = -37.55 +   0.88)

alignment

secondary structure

dotplot

Window 8

Location	21,269,225 – 21,269,345
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.64
Mean single sequence MFE	-38.46
Consensus MFE	-35.55
Energy contribution	-35.67
Covariance contribution	0.13
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.92
SVM decision value	1.30
SVM RNA-class probability	0.939537
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21269225 120 - 23771897
GUCCAAUCUUCCCUGUGAAAGGUGAACGCCCAUGUGGGUUAGAACUCUGGAUGAUGCUAUUAAGAUUUCCACAUACCUUUUUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCC
(((.....((((((.....))).))).(((((...((((..(((.(((.((((....)))).))).))).....))))...)))))...(((.((((((((...)))))))))))))).. ( -38.20)
>DroSec_CAF1 27502 120 - 1
GUCCAAUCUUCCCUGUGAAAGGUGAAGGCACAUGUGGAUUAGAACUCUGGAGGAUGACAUUAAGAUUUCCACAUACCUUUUUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCU
((((((((((((((.....))).)))))...(((((((((((....)))).(.....).........)))))))......)))))).(((((.((((((((...)))))))))))))... ( -39.60)
>DroSim_CAF1 29758 120 - 1
GUCCAAUCUUCCCUGUGAAAGGUGAAGGCCCAUGUGGGUUAGAACUCUGGAGGAUGACAUUAAGAUUUCCACAUACCUUUUUGGGCAUUGUCUAUUGCCCCUUUGGAGCGAUGACGACCU
(((....(((((((.....))).))))(((((...((((..(((.(((.((........)).))).))).....))))...)))))...(((.(((((((....)).))))))))))).. ( -35.70)
>DroEre_CAF1 28677 120 - 1
GUCCAAUCUUUCCUGUGGUAGGUGAAGUGCCAUGUGGGUUAGAGCUCUGGAGGAUCCCUUCAAGAUUUCCACAUACCUUUUUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCC
((((((..........(((((((.....))).((((((......((.((((((...))))))))...))))))))))...)))))).(((((.((((((((...)))))))))))))... ( -40.32)
>consensus
GUCCAAUCUUCCCUGUGAAAGGUGAAGGCCCAUGUGGGUUAGAACUCUGGAGGAUGACAUUAAGAUUUCCACAUACCUUUUUGGGCAUUGUCUAUUGCUCCUUUGGAGCGAUGACGACCC
((((((.(((((((.....))).))))....(((((((.......(((.((((....)))).)))..)))))))......)))))).(((((.((((((((...)))))))))))))... (-35.55 = -35.67 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:36 2006