Locus 9799

Sequence ID	3R_DroMel_CAF1
Location	26,032,893 – 26,033,022
Length	129
Max. P	0.977044

overview

Window 5

Location	26,032,893 – 26,033,000
Length	107
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	78.06
Mean single sequence MFE	-34.62
Consensus MFE	-23.44
Energy contribution	-23.00
Covariance contribution	-0.44
Combinations/Pair	1.39
Mean z-score	-2.06
Structure conservation index	0.68
SVM decision value	1.38
SVM RNA-class probability	0.947833
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26032893 107 + 27905053
GUAAUGCAGUAGCCGUUGA--GAGUCGGCUCAACAUUGUGGAGUGAUUAGCGGC-----AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCUUAGGU-AAUCGCUUAGCGAAU
((...((((.(((.(((((--(......))))))........(((((((((...-----.))))))).)))))))))...))..(((((((((......-....))))))))).. ( -36.20)
>DroVir_CAF1 43654 112 + 1
GUUAUGCAGAAGCCUUGGAAUUGAUAGGCUCUGCAACGUGGAGUAAACUG--UUCUGGGUUUCAAUAUGCGUUCUGUUUGACAAUCGCUGAACAAGAAU-AAAAGUUCAGCGAAU
((((.((((((((.(((((((((((((((((..(...)..))))...)))--))...))))))))...)).)))))).))))..(((((((((......-....))))))))).. ( -38.50)
>DroSec_CAF1 26015 107 + 1
GUAAUGCAGUAGCCGUGGA--GAGUCAGCUCAACAUUGUGGAGUGAUUAGCGGC-----AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCUUAGGU-AAUCGCUUAGCGAAU
((...((((..(((((...--.(((((.(((.((...)).)))))))).)))))-----.((......))...))))...))..(((((((((......-....))))))))).. ( -34.00)
>DroSim_CAF1 27647 107 + 1
GUAAUGCAGUAGCCGUGGA--GAGUCGGCUCAACAUUGUGGAGUGAUUAGCGGC-----AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCUUAGGU-AAUCGCUUAGCGAAU
((...((((..(((((...--.(((((.(((.((...)).)))))))).)))))-----.((......))...))))...))..(((((((((......-....))))))))).. ( -33.60)
>DroEre_CAF1 27084 107 + 1
GUAAUGCAGUAGCCGUGGC--AAGUCGGCUCAACAUUGUGGAGUGAUUAGCGGC-----CGUUAAUUUACGUUCUGUUUGACAAUCGCUGAGCUUGGGU-GAUCGCUUAGCGAAU
((...((((..(((((...--.(((((.(((.((...)).)))))))).)))))-----(((......)))..))))...))..(((((((((......-....))))))))).. ( -33.00)
>DroAna_CAF1 28550 115 + 1
GUAAUGCUGUAGUCCUGGAUAAAGUCGACUAAGCAUUAUGGAGUGAUUAGCUGCCUGGUGAUUAUUCUGCGUUCUGUUUGACAAUCACUAGGGUAGGAUGAAACACCUAGCAAAU
((((((((.(((((((......))..)))))))))))))((.((..(((.(((((((((((((.((..((.....))..)).)))))))).)))))..))).)).))........ ( -32.40)
>consensus
GUAAUGCAGUAGCCGUGGA__GAGUCGGCUCAACAUUGUGGAGUGAUUAGCGGC_____AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCUUAGGU_AAUCGCUUAGCGAAU
((...((((.(((((..........)))))......((((((.(((((...........))))).))))))..))))...))..(((((((((...........))))))))).. (-23.44 = -23.00 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	26,032,893 – 26,033,000
Length	107
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.06
Mean single sequence MFE	-25.02
Consensus MFE	-18.14
Energy contribution	-17.12
Covariance contribution	-1.02
Combinations/Pair	1.44
Mean z-score	-1.65
Structure conservation index	0.72
SVM decision value	1.04
SVM RNA-class probability	0.905913
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26032893 107 - 27905053
AUUCGCUAAGCGAUU-ACCUAAGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU-----GCCGCUAAUCACUCCACAAUGUUGAGCCGACUC--UCAACGGCUACUGCAUUAC
..(((((.(((....-......))).)))))..............((.(((((...-----.....))))))).....(((((..(((((....--....)))))...))))).. ( -24.60)
>DroVir_CAF1 43654 112 - 1
AUUCGCUGAACUUUU-AUUCUUGUUCAGCGAUUGUCAAACAGAACGCAUAUUGAAACCCAGAA--CAGUUUACUCCACGUUGCAGAGCCUAUCAAUUCCAAGGCUUCUGCAUAAC
..(((((((((....-......)))))))))...........((((.......((((......--..))))......))))(((((((((..........)))).)))))..... ( -29.12)
>DroSec_CAF1 26015 107 - 1
AUUCGCUAAGCGAUU-ACCUAAGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU-----GCCGCUAAUCACUCCACAAUGUUGAGCUGACUC--UCCACGGCUACUGCAUUAC
..(((((.(((....-......))).)))))..............((.(((((...-----.....))))))).....(((((..(((((....--....)))))...))))).. ( -22.40)
>DroSim_CAF1 27647 107 - 1
AUUCGCUAAGCGAUU-ACCUAAGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU-----GCCGCUAAUCACUCCACAAUGUUGAGCCGACUC--UCCACGGCUACUGCAUUAC
..(((((.(((....-......))).)))))..............((.(((((...-----.....))))))).....(((((..(((((....--....)))))...))))).. ( -24.60)
>DroEre_CAF1 27084 107 - 1
AUUCGCUAAGCGAUC-ACCCAAGCUCAGCGAUUGUCAAACAGAACGUAAAUUAACG-----GCCGCUAAUCACUCCACAAUGUUGAGCCGACUU--GCCACGGCUACUGCAUUAC
..(((((.(((....-......))).)))))..........(..(((......)))-----..)..............(((((..(((((....--....)))))...))))).. ( -24.40)
>DroAna_CAF1 28550 115 - 1
AUUUGCUAGGUGUUUCAUCCUACCCUAGUGAUUGUCAAACAGAACGCAGAAUAAUCACCAGGCAGCUAAUCACUCCAUAAUGCUUAGUCGACUUUAUCCAGGACUACAGCAUUAC
....((((((........)))..(((.(((((((((............).)))))))).))).)))...........((((((((((((............))))).))))))). ( -25.00)
>consensus
AUUCGCUAAGCGAUU_ACCCAAGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU_____GCCGCUAAUCACUCCACAAUGUUGAGCCGACUC__UCCACGGCUACUGCAUUAC
..(((((.(((...........))).)))))...............................................(((((..(((((..........)))))...))))).. (-18.14 = -17.12 +  -1.02)

alignment

secondary structure

dotplot

Window 7

Location	26,032,931 – 26,033,022
Length	91
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	75.80
Mean single sequence MFE	-25.48
Consensus MFE	-19.26
Energy contribution	-18.54
Covariance contribution	-0.72
Combinations/Pair	1.30
Mean z-score	-1.78
Structure conservation index	0.76
SVM decision value	1.63
SVM RNA-class probability	0.969008
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26032931 91 + 27905053
GAGUGAUUAGCGGC-----AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCU--UAGGU-AAUCGCUUAGCGAAUAACACAAGAACGGAGUUCACAA
(((.(((((((...-----.)))))))..((((((...((....(((((((((.--.....-....)))))))))....))..))))))...))).... ( -28.30)
>DroPse_CAF1 29834 96 + 1
GAGUGAGUAGUUGCUUUGAGUUUACUGUACGUUCUGUUUGACAAUCACAGGACUAUAAGGU-GA--GUCCAGUGAAUAACACAAGAACGGCGGAUAUAA
(((..(....)..)))........((((.((((((...((....((((.(((((.......-.)--)))).))))....))..))))))))))...... ( -23.90)
>DroSim_CAF1 27685 91 + 1
GAGUGAUUAGCGGC-----AGUUAAUCUACGUUCUGUUUGACAAUCGCUGAGCU--UAGGU-AAUCGCUUAGCGAAUAACACAAGAACGGAGUUCACAA
(((.(((((((...-----.)))))))..((((((...((....(((((((((.--.....-....)))))))))....))..))))))...))).... ( -28.30)
>DroEre_CAF1 27122 91 + 1
GAGUGAUUAGCGGC-----CGUUAAUUUACGUUCUGUUUGACAAUCGCUGAGCU--UGGGU-GAUCGCUUAGCGAAUAACACAAGAACGGUAUUUACAA
..(((((((((...-----.)))))....((((((...((....(((((((((.--.....-....)))))))))....))..))))))....)))).. ( -25.50)
>DroAna_CAF1 28590 93 + 1
GAGUGAUUAGCUGCCUGGUGAUUAUUCUGCGUUCUGUUUGACAAUCACUAGGGU--AGGAUGAAACACCUAGCAAAUAACACAAGAACGGU----ACAG
..(((.(((..(((..((((.(((((((((..((((..((.....)).))))))--)))))))..))))..)))..)))))).........----.... ( -23.00)
>DroPer_CAF1 30482 96 + 1
GAGUGAGUAGUUGCUUUGAGUUUACUGUACGUUCUGUUUGACAAUCACAGGACUAUAAGGU-GA--GUCCAGUGAAUAACACAAGAACGGCGGAUAUAA
(((..(....)..)))........((((.((((((...((....((((.(((((.......-.)--)))).))))....))..))))))))))...... ( -23.90)
>consensus
GAGUGAUUAGCGGC_____GGUUAAUCUACGUUCUGUUUGACAAUCACUGAGCU__AAGGU_AAUCGCCUAGCGAAUAACACAAGAACGGAGUUUACAA
....((((((...........))))))..((((((...((....(((((((((.............)))))))))....))..)))))).......... (-19.26 = -18.54 +  -0.72)

alignment

secondary structure

dotplot

Window 8

Location	26,032,931 – 26,033,022
Length	91
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	75.80
Mean single sequence MFE	-21.20
Consensus MFE	-16.19
Energy contribution	-15.14
Covariance contribution	-1.05
Combinations/Pair	1.28
Mean z-score	-1.92
Structure conservation index	0.76
SVM decision value	1.78
SVM RNA-class probability	0.977044
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26032931 91 - 27905053
UUGUGAACUCCGUUCUUGUGUUAUUCGCUAAGCGAUU-ACCUA--AGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU-----GCCGCUAAUCACUC
..((((.....(((((..((.((.(((((.(((....-.....--.))).))))).)).))...)))))((((.....))-----))......)))).. ( -23.70)
>DroPse_CAF1 29834 96 - 1
UUAUAUCCGCCGUUCUUGUGUUAUUCACUGGAC--UC-ACCUUAUAGUCCUGUGAUUGUCAAACAGAACGUACAGUAAACUCAAAGCAACUACUCACUC
........((((((((..((.((.((((.((((--(.-.......))))).)))).)).))...))))))...((....))....))............ ( -19.90)
>DroSim_CAF1 27685 91 - 1
UUGUGAACUCCGUUCUUGUGUUAUUCGCUAAGCGAUU-ACCUA--AGCUCAGCGAUUGUCAAACAGAACGUAGAUUAACU-----GCCGCUAAUCACUC
..((((.....(((((..((.((.(((((.(((....-.....--.))).))))).)).))...)))))((((.....))-----))......)))).. ( -23.70)
>DroEre_CAF1 27122 91 - 1
UUGUAAAUACCGUUCUUGUGUUAUUCGCUAAGCGAUC-ACCCA--AGCUCAGCGAUUGUCAAACAGAACGUAAAUUAACG-----GCCGCUAAUCACUC
.(((.(((..((((((..((.((.(((((.(((....-.....--.))).))))).)).))...))))))...))).)))-----.............. ( -19.40)
>DroAna_CAF1 28590 93 - 1
CUGU----ACCGUUCUUGUGUUAUUUGCUAGGUGUUUCAUCCU--ACCCUAGUGAUUGUCAAACAGAACGCAGAAUAAUCACCAGGCAGCUAAUCACUC
((((----..((((((..((.((.(..(((((.((........--)))))))..).)).))...))))))..((....)).....)))).......... ( -20.60)
>DroPer_CAF1 30482 96 - 1
UUAUAUCCGCCGUUCUUGUGUUAUUCACUGGAC--UC-ACCUUAUAGUCCUGUGAUUGUCAAACAGAACGUACAGUAAACUCAAAGCAACUACUCACUC
........((((((((..((.((.((((.((((--(.-.......))))).)))).)).))...))))))...((....))....))............ ( -19.90)
>consensus
UUGUAAACACCGUUCUUGUGUUAUUCGCUAAGCGAUC_ACCUA__AGCCCAGCGAUUGUCAAACAGAACGUAGAUUAACC_____GCAGCUAAUCACUC
..........((((((..((.((.(((((.(((.............))).))))).)).))...))))))............................. (-16.19 = -15.14 +  -1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:42:25 2006